Starting phenix.real_space_refine on Thu May 16 20:16:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgq_19146/05_2024/8rgq_19146_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgq_19146/05_2024/8rgq_19146.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgq_19146/05_2024/8rgq_19146_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgq_19146/05_2024/8rgq_19146_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgq_19146/05_2024/8rgq_19146_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgq_19146/05_2024/8rgq_19146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgq_19146/05_2024/8rgq_19146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgq_19146/05_2024/8rgq_19146_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgq_19146/05_2024/8rgq_19146_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 42 5.49 5 Mg 1 5.21 5 S 492 5.16 5 C 43405 2.51 5 N 11105 2.21 5 O 12043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 373": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "7 GLU 78": "OE1" <-> "OE2" Residue "7 PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "W GLU 113": "OE1" <-> "OE2" Residue "q PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "L GLU 397": "OE1" <-> "OE2" Residue "O GLU 268": "OE1" <-> "OE2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 33": "OE1" <-> "OE2" Residue "g GLU 85": "OE1" <-> "OE2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "k TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 56": "OE1" <-> "OE2" Residue "o GLU 19": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 67118 Number of models: 1 Model: "" Number of chains: 67 Chain: "6" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 146} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1730 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "D" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3371 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 25, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1660 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 192} Chain: "1" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3321 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "3" Number of atoms: 5305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5305 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 31, 'TRANS': 658} Chain: "9" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 168} Chain: "P" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2513 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 15, 'TRANS': 298} Chain breaks: 2 Chain: "Q" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1022 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "7" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "S" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 671 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 923 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "q" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "r" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "A" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 760 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'FME:plan-2': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2452 Classifications: {'peptide': 306} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1246 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3632 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2703 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 324} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2607 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "U" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 706 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "X" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1396 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain: "Y" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1037 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "Z" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1167 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "a" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 572 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "b" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 643 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 11, 'TRANS': 70} Chain: "c" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 398 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 996 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain: "e" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 877 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "f" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 456 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 850 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1166 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain: "i" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 897 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 562 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 6, 'TRANS': 58} Chain: "k" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "l" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1323 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 18, 'TRANS': 138} Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 11, 'TRANS': 114} Chain: "n" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1541 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "o" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1014 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 110} Chain: "p" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1430 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 10, 'TRANS': 158} Chain: "6" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "9" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'PC1': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "r" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "L" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 180 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "M" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'3PE': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "N" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 128 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'DGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "d" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 130 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 Chain: "h" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 70 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "m" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "n" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 766 SG CYS 6 129 62.649 129.487 109.066 1.00 74.44 S ATOM 269 SG CYS 6 65 57.439 126.843 105.904 1.00 88.44 S ATOM 263 SG CYS 6 64 59.066 124.144 111.222 1.00 73.98 S ATOM 996 SG CYS 6 159 56.919 130.218 111.547 1.00 77.51 S ATOM 7165 SG CYS 2 103 26.361 167.280 163.237 1.00 59.51 S ATOM 7199 SG CYS 2 108 23.830 166.551 165.638 1.00 57.15 S ATOM 7483 SG CYS 2 144 30.510 166.485 166.715 1.00 68.62 S ATOM 7506 SG CYS 2 148 28.366 165.660 169.357 1.00 65.53 S ATOM 10744 SG CYS 1 365 42.959 158.152 157.058 1.00 87.11 S ATOM 11066 SG CYS 1 405 46.134 160.613 162.152 1.00 74.63 S ATOM 10724 SG CYS 1 362 48.405 157.785 156.457 1.00 66.53 S ATOM 10705 SG CYS 1 359 46.250 164.178 156.978 1.00 97.90 S ATOM 12170 SG CYS 3 114 54.766 152.676 137.342 1.00 69.89 S ATOM 12109 SG CYS 3 105 49.713 150.423 133.874 1.00 76.92 S ATOM 12130 SG CYS 3 108 52.134 156.335 132.658 1.00127.23 S ATOM 12502 SG CYS 3 156 55.780 160.972 145.402 1.00 78.55 S ATOM 12479 SG CYS 3 153 50.001 163.073 142.774 1.00114.14 S ATOM 12526 SG CYS 3 159 55.087 167.051 143.101 1.00 70.40 S ATOM 12855 SG CYS 3 203 55.340 161.844 139.196 1.00 86.50 S ATOM 11616 SG CYS 3 41 57.364 158.612 151.725 1.00 68.22 S ATOM 11702 SG CYS 3 52 55.781 155.385 150.544 1.00 91.01 S ATOM 11727 SG CYS 3 55 59.344 153.479 155.142 1.00 84.97 S ATOM 11828 SG CYS 3 69 60.089 157.077 155.156 1.00 75.40 S ATOM 17616 SG CYS 9 121 53.987 134.992 117.992 1.00 85.60 S ATOM 17590 SG CYS 9 118 54.012 137.279 111.766 1.00 77.55 S ATOM 17637 SG CYS 9 124 50.804 140.337 116.485 1.00 81.01 S ATOM 17364 SG CYS 9 89 57.367 140.309 116.427 1.00 93.44 S ATOM 17666 SG CYS 9 128 46.470 146.008 120.429 1.00 83.61 S ATOM 17336 SG CYS 9 85 52.722 146.203 118.648 1.00 87.43 S ATOM 17294 SG CYS 9 79 49.042 151.459 117.663 1.00 85.26 S ATOM 17313 SG CYS 9 82 50.377 149.295 123.860 1.00 75.80 S ATOM 22091 SG CYS 7 59 35.255 156.035 126.517 1.00 82.61 S ATOM 22267 SG CYS 7 84 39.136 157.085 126.140 1.00 72.38 S ATOM 22289 SG CYS 7 87 37.113 156.709 123.510 1.00 90.37 S Time building chain proxies: 25.49, per 1000 atoms: 0.38 Number of scatterers: 67118 At special positions: 0 Unit cell: (236.38, 209.88, 212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 492 16.00 P 42 15.00 Mg 1 11.99 O 12043 8.00 N 11105 7.00 C 43405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.04 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.03 Simple disulfide: pdb=" SG CYS o 58 " - pdb=" SG CYS o 89 " distance=2.03 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.11 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 301 " pdb="FE1 FES 2 301 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 301 " - pdb=" SG CYS 2 148 " pdb="FE2 FES 2 301 " - pdb=" SG CYS 2 144 " pdb="FE1 FES 2 301 " - pdb=" SG CYS 2 108 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 502 " pdb="FE1 SF4 1 502 " - pdb=" SG CYS 1 365 " pdb="FE2 SF4 1 502 " - pdb=" SG CYS 1 405 " pdb="FE3 SF4 1 502 " - pdb=" SG CYS 1 362 " pdb="FE4 SF4 1 502 " - pdb=" SG CYS 1 359 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb=" SF4 6 201 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 64 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 129 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 159 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 65 " pdb=" SF4 9 201 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 124 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 118 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 89 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 121 " pdb="FE3 SF4 9 201 " - pdb=" NE2 HIS 9 67 " pdb=" SF4 9 202 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 82 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 85 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 79 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 128 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN 7 201 " pdb="ZN ZN 7 201 " - pdb=" NE2 HIS 7 68 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 87 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 84 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 59 " Number of angles added : 3 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 331 helices and 28 sheets defined 52.9% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.12 Creating SS restraints... Processing helix chain '6' and resid 35 through 53 Processing helix chain '6' and resid 64 through 73 Processing helix chain '6' and resid 79 through 82 No H-bonds generated for 'chain '6' and resid 79 through 82' Processing helix chain '6' and resid 90 through 92 No H-bonds generated for 'chain '6' and resid 90 through 92' Processing helix chain '6' and resid 104 through 116 Proline residue: 6 108 - end of helix Processing helix chain '6' and resid 128 through 132 Processing helix chain '6' and resid 134 through 136 No H-bonds generated for 'chain '6' and resid 134 through 136' Processing helix chain '6' and resid 146 through 148 No H-bonds generated for 'chain '6' and resid 146 through 148' Processing helix chain '6' and resid 163 through 178 Processing helix chain '6' and resid 182 through 188 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.675A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 14 removed outlier: 4.308A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 Processing helix chain 'D' and resid 96 through 106 Proline residue: D 101 - end of helix removed outlier: 4.030A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 Processing helix chain 'D' and resid 207 through 227 removed outlier: 4.037A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 293 through 316 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 400 Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 411 through 420 Processing helix chain 'D' and resid 425 through 429 Processing helix chain '2' and resid 25 through 37 Processing helix chain '2' and resid 43 through 58 removed outlier: 3.562A pdb=" N VAL 2 47 " --> pdb=" O ALA 2 44 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 63 through 73 Processing helix chain '2' and resid 77 through 86 Processing helix chain '2' and resid 106 through 110 Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 166 through 178 Processing helix chain '1' and resid 33 through 39 Processing helix chain '1' and resid 45 through 63 Proline residue: 1 53 - end of helix Processing helix chain '1' and resid 75 through 82 removed outlier: 4.498A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 129 Processing helix chain '1' and resid 143 through 159 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 197 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 237 Proline residue: 1 232 - end of helix Processing helix chain '1' and resid 239 through 244 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 309 through 312 No H-bonds generated for 'chain '1' and resid 309 through 312' Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 357 Processing helix chain '1' and resid 363 through 381 Processing helix chain '1' and resid 386 through 399 Processing helix chain '1' and resid 407 through 421 Proline residue: 1 414 - end of helix Processing helix chain '1' and resid 423 through 437 Processing helix chain '3' and resid 26 through 33 Processing helix chain '3' and resid 84 through 100 removed outlier: 4.125A pdb=" N ASN 3 100 " --> pdb=" O PHE 3 96 " (cutoff:3.500A) Processing helix chain '3' and resid 115 through 123 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 198 through 202 Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 271 through 275 Processing helix chain '3' and resid 296 through 309 Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 362 Processing helix chain '3' and resid 367 through 373 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 Processing helix chain '3' and resid 438 through 445 Processing helix chain '3' and resid 455 through 458 No H-bonds generated for 'chain '3' and resid 455 through 458' Processing helix chain '3' and resid 463 through 481 Processing helix chain '3' and resid 497 through 505 removed outlier: 4.653A pdb=" N ALA 3 501 " --> pdb=" O ALA 3 497 " (cutoff:3.500A) Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 607 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 642 through 651 Processing helix chain '3' and resid 668 through 672 Processing helix chain '3' and resid 676 through 680 Processing helix chain '3' and resid 682 through 692 Processing helix chain '9' and resid 16 through 28 Processing helix chain '9' and resid 30 through 44 Processing helix chain '9' and resid 84 through 88 Processing helix chain '9' and resid 123 through 127 Processing helix chain '9' and resid 147 through 149 No H-bonds generated for 'chain '9' and resid 147 through 149' Processing helix chain '9' and resid 153 through 162 Processing helix chain '9' and resid 164 through 174 removed outlier: 4.386A pdb=" N ALA 9 169 " --> pdb=" O ALA 9 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 41 removed outlier: 4.166A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 4.444A pdb=" N LEU P 61 " --> pdb=" O HIS P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 85 Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 187 removed outlier: 4.363A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 249 Processing helix chain 'P' and resid 281 through 288 Processing helix chain 'P' and resid 315 through 321 removed outlier: 5.439A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 324 through 327 No H-bonds generated for 'chain 'P' and resid 324 through 327' Processing helix chain 'Q' and resid 20 through 23 No H-bonds generated for 'chain 'Q' and resid 20 through 23' Processing helix chain 'Q' and resid 28 through 31 No H-bonds generated for 'chain 'Q' and resid 28 through 31' Processing helix chain 'Q' and resid 50 through 52 No H-bonds generated for 'chain 'Q' and resid 50 through 52' Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain '7' and resid 23 through 27 removed outlier: 3.743A pdb=" N ARG 7 27 " --> pdb=" O ARG 7 24 " (cutoff:3.500A) Processing helix chain '7' and resid 40 through 45 Processing helix chain '7' and resid 64 through 66 No H-bonds generated for 'chain '7' and resid 64 through 66' Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.585A pdb=" N TYR S 40 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL S 41 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU S 42 " --> pdb=" O GLN S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 8 through 21 Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 68 removed outlier: 4.157A pdb=" N GLU T 68 " --> pdb=" O ASP T 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 68' Processing helix chain 'T' and resid 73 through 83 Processing helix chain 'V' and resid 19 through 36 removed outlier: 3.995A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 Processing helix chain 'W' and resid 27 through 51 Proline residue: W 46 - end of helix Processing helix chain 'W' and resid 58 through 74 removed outlier: 4.573A pdb=" N HIS W 74 " --> pdb=" O MET W 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 96 Processing helix chain 'W' and resid 102 through 108 removed outlier: 4.299A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'q' and resid 2 through 16 Processing helix chain 'q' and resid 20 through 29 Processing helix chain 'q' and resid 84 through 91 Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 'r' and resid 59 through 61 No H-bonds generated for 'chain 'r' and resid 59 through 61' Processing helix chain 's' and resid 35 through 37 No H-bonds generated for 'chain 's' and resid 35 through 37' Processing helix chain 's' and resid 44 through 55 removed outlier: 4.506A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE s 55 " --> pdb=" O ASP s 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.629A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 87 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 Processing helix chain 'H' and resid 126 through 157 Processing helix chain 'H' and resid 163 through 169 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 193 Processing helix chain 'H' and resid 218 through 242 Processing helix chain 'H' and resid 253 through 276 Processing helix chain 'H' and resid 282 through 311 removed outlier: 5.405A pdb=" N LEU H 294 " --> pdb=" O TRP H 290 " (cutoff:3.500A) Proline residue: H 295 - end of helix Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 4 through 21 Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 73 Processing helix chain 'J' and resid 87 through 109 Processing helix chain 'J' and resid 138 through 143 Processing helix chain 'J' and resid 149 through 169 Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 58 through 85 Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 3 through 24 Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 27 through 29 No H-bonds generated for 'chain 'L' and resid 27 through 29' Processing helix chain 'L' and resid 32 through 57 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 157 Processing helix chain 'L' and resid 162 through 193 Processing helix chain 'L' and resid 198 through 206 removed outlier: 5.062A pdb=" N ASN L 206 " --> pdb=" O MET L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 232 through 238 removed outlier: 4.673A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 3.890A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.936A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 292 Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 388 through 390 No H-bonds generated for 'chain 'L' and resid 388 through 390' Processing helix chain 'L' and resid 392 through 401 Processing helix chain 'L' and resid 406 through 431 Processing helix chain 'L' and resid 448 through 471 Proline residue: L 453 - end of helix removed outlier: 6.160A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 561 removed outlier: 3.810A pdb=" N PHE L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 3.692A pdb=" N ILE L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.612A pdb=" N LEU L 542 " --> pdb=" O MET L 539 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN L 543 " --> pdb=" O LYS L 540 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU L 546 " --> pdb=" O ASN L 543 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS L 547 " --> pdb=" O LEU L 544 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR L 548 " --> pdb=" O SER L 545 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER L 549 " --> pdb=" O LEU L 546 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU L 550 " --> pdb=" O LYS L 547 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR L 551 " --> pdb=" O THR L 548 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU L 552 " --> pdb=" O SER L 549 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU L 553 " --> pdb=" O LEU L 550 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP L 554 " --> pdb=" O THR L 551 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU L 555 " --> pdb=" O LEU L 552 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE L 556 " --> pdb=" O LEU L 553 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TRP L 557 " --> pdb=" O ASP L 554 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU L 558 " --> pdb=" O LEU L 555 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU L 559 " --> pdb=" O ILE L 556 " (cutoff:3.500A) Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 605 Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.195A pdb=" N LEU M 12 " --> pdb=" O SER M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 4.237A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 81 Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 136 Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 142 through 171 Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 181 Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.446A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 4.318A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 250 removed outlier: 5.590A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.624A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 277 Processing helix chain 'M' and resid 282 through 303 Processing helix chain 'M' and resid 306 through 337 Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 414 removed outlier: 3.760A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE M 394 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET M 408 " --> pdb=" O MET M 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR M 414 " --> pdb=" O ILE M 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 454 removed outlier: 3.696A pdb=" N ILE M 454 " --> pdb=" O PRO M 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 451 through 454' Processing helix chain 'N' and resid 3 through 22 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 119 Processing helix chain 'N' and resid 124 through 148 removed outlier: 5.665A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.702A pdb=" N ILE N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR N 146 " --> pdb=" O LEU N 142 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 Processing helix chain 'N' and resid 175 through 194 Processing helix chain 'N' and resid 198 through 222 Proline residue: N 214 - end of helix removed outlier: 4.155A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.184A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS N 236 " --> pdb=" O LEU N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.684A pdb=" N LEU N 241 " --> pdb=" O PRO N 238 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET N 247 " --> pdb=" O ILE N 244 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 276 through 300 Processing helix chain 'N' and resid 311 through 316 Processing helix chain 'N' and resid 324 through 334 removed outlier: 3.618A pdb=" N SER N 327 " --> pdb=" O LEU N 324 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR N 328 " --> pdb=" O MET N 325 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU N 329 " --> pdb=" O PHE N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 343 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 11 Processing helix chain 'O' and resid 14 through 17 No H-bonds generated for 'chain 'O' and resid 14 through 17' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 128 through 130 No H-bonds generated for 'chain 'O' and resid 128 through 130' Processing helix chain 'O' and resid 132 through 140 Processing helix chain 'O' and resid 146 through 162 Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 196 through 215 removed outlier: 4.921A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix Processing helix chain 'O' and resid 233 through 239 Processing helix chain 'O' and resid 253 through 264 Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 272 through 274 No H-bonds generated for 'chain 'O' and resid 272 through 274' Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 69 Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 34 Processing helix chain 'X' and resid 36 through 48 Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 56 through 76 Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 101 through 112 Processing helix chain 'Y' and resid 2 through 5 No H-bonds generated for 'chain 'Y' and resid 2 through 5' Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 80 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 31 through 96 Proline residue: Z 72 - end of helix Processing helix chain 'Z' and resid 120 through 124 Processing helix chain 'Z' and resid 129 through 141 removed outlier: 6.288A pdb=" N PHE Z 139 " --> pdb=" O ALA Z 135 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR Z 140 " --> pdb=" O ASN Z 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 31 removed outlier: 3.586A pdb=" N ILE a 5 " --> pdb=" O TRP a 2 " (cutoff:3.500A) Proline residue: a 7 - end of helix removed outlier: 4.536A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.518A pdb=" N SER a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 3 through 14 Processing helix chain 'b' and resid 16 through 33 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 4.084A pdb=" N SER b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 81 No H-bonds generated for 'chain 'b' and resid 78 through 81' Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'e' and resid 47 through 54 Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 88 Processing helix chain 'f' and resid 6 through 9 No H-bonds generated for 'chain 'f' and resid 6 through 9' Processing helix chain 'f' and resid 11 through 33 removed outlier: 3.707A pdb=" N ILE f 14 " --> pdb=" O TRP f 11 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU f 15 " --> pdb=" O VAL f 12 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix Processing helix chain 'g' and resid 35 through 38 No H-bonds generated for 'chain 'g' and resid 35 through 38' Processing helix chain 'g' and resid 49 through 63 Processing helix chain 'g' and resid 70 through 76 Processing helix chain 'g' and resid 81 through 100 removed outlier: 3.707A pdb=" N GLN g 84 " --> pdb=" O TYR g 81 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLU g 85 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP g 86 " --> pdb=" O MET g 83 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU g 90 " --> pdb=" O ALA g 87 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG g 98 " --> pdb=" O VAL g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 113 through 115 No H-bonds generated for 'chain 'g' and resid 113 through 115' Processing helix chain 'h' and resid 16 through 46 Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 64 through 66 No H-bonds generated for 'chain 'h' and resid 64 through 66' Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 116 Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 24 Processing helix chain 'i' and resid 65 through 72 removed outlier: 3.888A pdb=" N PHE i 69 " --> pdb=" O ARG i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 88 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 24 through 26 No H-bonds generated for 'chain 'k' and resid 24 through 26' Processing helix chain 'k' and resid 33 through 44 removed outlier: 3.596A pdb=" N ARG k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.350A pdb=" N TRP k 56 " --> pdb=" O ASN k 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG k 57 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 62 No H-bonds generated for 'chain 'k' and resid 60 through 62' Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 76 through 93 Processing helix chain 'l' and resid 16 through 25 Processing helix chain 'l' and resid 80 through 83 No H-bonds generated for 'chain 'l' and resid 80 through 83' Processing helix chain 'l' and resid 97 through 120 Processing helix chain 'l' and resid 133 through 141 removed outlier: 5.961A pdb=" N LEU l 139 " --> pdb=" O ASN l 135 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU l 140 " --> pdb=" O ASN l 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 51 Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 74 through 77 No H-bonds generated for 'chain 'm' and resid 74 through 77' Processing helix chain 'm' and resid 83 through 116 Proline residue: m 96 - end of helix Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 57 through 72 Processing helix chain 'n' and resid 100 through 105 removed outlier: 3.507A pdb=" N LEU n 103 " --> pdb=" O GLU n 100 " (cutoff:3.500A) Processing helix chain 'n' and resid 108 through 142 removed outlier: 3.720A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.632A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 2 through 8 Processing helix chain 'o' and resid 42 through 48 Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 117 Processing helix chain 'p' and resid 28 through 57 removed outlier: 5.207A pdb=" N TRP p 42 " --> pdb=" O LEU p 38 " (cutoff:3.500A) Proline residue: p 43 - end of helix Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 6.657A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 168 Processing sheet with id= A, first strand: chain '6' and resid 57 through 61 removed outlier: 6.100A pdb=" N VAL 6 95 " --> pdb=" O MET 6 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE 6 60 " --> pdb=" O VAL 6 95 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE 6 97 " --> pdb=" O PHE 6 60 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR 6 122 " --> pdb=" O MET 6 96 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL 6 98 " --> pdb=" O TYR 6 122 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL 6 124 " --> pdb=" O VAL 6 98 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE 6 154 " --> pdb=" O SER 6 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.526A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ILE C 52 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 Processing sheet with id= F, first strand: chain '2' and resid 137 through 142 removed outlier: 6.358A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 219 through 224 removed outlier: 6.173A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '1' and resid 266 through 271 Processing sheet with id= I, first strand: chain '3' and resid 8 through 13 Processing sheet with id= J, first strand: chain '3' and resid 146 through 148 Processing sheet with id= K, first strand: chain '3' and resid 173 through 175 Processing sheet with id= L, first strand: chain '3' and resid 223 through 228 removed outlier: 6.271A pdb=" N ARG 3 243 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL 3 247 " --> pdb=" O ARG 3 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 283 through 285 Processing sheet with id= N, first strand: chain '3' and resid 343 through 345 removed outlier: 8.456A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain '3' and resid 490 through 493 removed outlier: 8.052A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '3' and resid 571 through 574 Processing sheet with id= Q, first strand: chain '9' and resid 67 through 69 Processing sheet with id= R, first strand: chain '9' and resid 94 through 100 removed outlier: 5.865A pdb=" N GLU 9 99 " --> pdb=" O THR 9 108 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR 9 108 " --> pdb=" O GLU 9 99 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.814A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= U, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= V, first strand: chain '7' and resid 50 through 52 Processing sheet with id= W, first strand: chain '7' and resid 56 through 59 Processing sheet with id= X, first strand: chain 'S' and resid 51 through 57 removed outlier: 6.538A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS S 63 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.540A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'L' and resid 61 through 67 removed outlier: 7.141A pdb=" N MET L 78 " --> pdb=" O THR L 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 219 through 223 removed outlier: 6.167A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) 2984 hydrogen bonds defined for protein. 8463 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.74 Time building geometry restraints manager: 22.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 28096 1.42 - 1.64: 39795 1.64 - 1.86: 804 1.86 - 2.09: 0 2.09 - 2.31: 80 Bond restraints: 68775 Sorted by residual: bond pdb=" C2' DGT O 401 " pdb=" C3' DGT O 401 " ideal model delta sigma weight residual 1.284 1.523 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C4' DGT O 401 " pdb=" O4' DGT O 401 " ideal model delta sigma weight residual 1.272 1.446 -0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" C4 DGT O 401 " pdb=" N3 DGT O 401 " ideal model delta sigma weight residual 1.502 1.345 0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C13 ZMP W 201 " pdb=" N1 ZMP W 201 " ideal model delta sigma weight residual 1.487 1.338 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C13 ZMP n 201 " pdb=" N1 ZMP n 201 " ideal model delta sigma weight residual 1.487 1.339 0.148 2.00e-02 2.50e+03 5.44e+01 ... (remaining 68770 not shown) Histogram of bond angle deviations from ideal: 68.79 - 82.37: 76 82.37 - 95.95: 3 95.95 - 109.54: 7855 109.54 - 123.12: 81514 123.12 - 136.70: 3569 Bond angle restraints: 93017 Sorted by residual: angle pdb=" PA NDP P 501 " pdb=" O3 NDP P 501 " pdb=" PN NDP P 501 " ideal model delta sigma weight residual 107.74 132.13 -24.39 1.95e+00 2.62e-01 1.56e+02 angle pdb=" C5B NDP P 501 " pdb=" O5B NDP P 501 " pdb=" PA NDP P 501 " ideal model delta sigma weight residual 103.84 119.10 -15.26 1.91e+00 2.73e-01 6.35e+01 angle pdb=" C5D NDP P 501 " pdb=" O5D NDP P 501 " pdb=" PN NDP P 501 " ideal model delta sigma weight residual 104.93 124.38 -19.45 2.66e+00 1.41e-01 5.35e+01 angle pdb=" O2X NDP P 501 " pdb=" P2B NDP P 501 " pdb=" O3X NDP P 501 " ideal model delta sigma weight residual 117.33 108.14 9.19 1.48e+00 4.57e-01 3.86e+01 angle pdb=" C SER J 84 " pdb=" N ASN J 85 " pdb=" CA ASN J 85 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 ... (remaining 93012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 40743 35.21 - 70.42: 860 70.42 - 105.62: 83 105.62 - 140.83: 3 140.83 - 176.04: 3 Dihedral angle restraints: 41692 sinusoidal: 17916 harmonic: 23776 Sorted by residual: dihedral pdb=" CB CYS X 45 " pdb=" SG CYS X 45 " pdb=" SG CYS X 55 " pdb=" CB CYS X 55 " ideal model delta sinusoidal sigma weight residual 93.00 165.58 -72.58 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" C10 FMN 1 501 " pdb=" C1' FMN 1 501 " pdb=" N10 FMN 1 501 " pdb=" C2' FMN 1 501 " ideal model delta sinusoidal sigma weight residual 257.59 81.55 176.04 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA PRO 6 57 " pdb=" C PRO 6 57 " pdb=" N MET 6 58 " pdb=" CA MET 6 58 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 41689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.243: 10098 4.243 - 8.485: 0 8.485 - 12.728: 0 12.728 - 16.971: 0 16.971 - 21.214: 24 Chirality restraints: 10122 Sorted by residual: chirality pdb="FE2 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S3 SF4 6 201 " pdb=" S4 SF4 6 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.66 21.21 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 9 201 " pdb=" S2 SF4 9 201 " pdb=" S3 SF4 9 201 " pdb=" S4 SF4 9 201 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 9 202 " pdb=" S2 SF4 9 202 " pdb=" S3 SF4 9 202 " pdb=" S4 SF4 9 202 " both_signs ideal model delta sigma weight residual False -10.55 10.59 -21.14 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10119 not shown) Planarity restraints: 11606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN 1 501 " -0.080 2.00e-02 2.50e+03 4.29e-02 8.73e+01 pdb=" C10 FMN 1 501 " -0.029 2.00e-02 2.50e+03 pdb=" C2 FMN 1 501 " 0.039 2.00e-02 2.50e+03 pdb=" C4 FMN 1 501 " -0.014 2.00e-02 2.50e+03 pdb=" C4A FMN 1 501 " -0.039 2.00e-02 2.50e+03 pdb=" C5A FMN 1 501 " -0.030 2.00e-02 2.50e+03 pdb=" C6 FMN 1 501 " -0.010 2.00e-02 2.50e+03 pdb=" C7 FMN 1 501 " 0.021 2.00e-02 2.50e+03 pdb=" C7M FMN 1 501 " 0.068 2.00e-02 2.50e+03 pdb=" C8 FMN 1 501 " 0.022 2.00e-02 2.50e+03 pdb=" C8M FMN 1 501 " 0.033 2.00e-02 2.50e+03 pdb=" C9 FMN 1 501 " 0.002 2.00e-02 2.50e+03 pdb=" C9A FMN 1 501 " -0.023 2.00e-02 2.50e+03 pdb=" N1 FMN 1 501 " 0.002 2.00e-02 2.50e+03 pdb=" N10 FMN 1 501 " -0.029 2.00e-02 2.50e+03 pdb=" N3 FMN 1 501 " 0.026 2.00e-02 2.50e+03 pdb=" N5 FMN 1 501 " -0.046 2.00e-02 2.50e+03 pdb=" O2 FMN 1 501 " 0.110 2.00e-02 2.50e+03 pdb=" O4 FMN 1 501 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS P 335 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO P 336 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO P 336 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO P 336 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU h 49 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" CD GLU h 49 " 0.062 2.00e-02 2.50e+03 pdb=" OE1 GLU h 49 " -0.022 2.00e-02 2.50e+03 pdb=" OE2 GLU h 49 " -0.022 2.00e-02 2.50e+03 ... (remaining 11603 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 6938 2.75 - 3.35: 78747 3.35 - 3.94: 139894 3.94 - 4.54: 193516 4.54 - 5.14: 286973 Nonbonded interactions: 706068 Sorted by model distance: nonbonded pdb=" OE1 GLU D 226 " pdb=" OG1 THR D 230 " model vdw 2.151 2.440 nonbonded pdb=" O1G DGT O 401 " pdb="MG MG O 402 " model vdw 2.175 2.170 nonbonded pdb=" OG SER H 110 " pdb=" OE2 GLU H 143 " model vdw 2.180 2.440 nonbonded pdb=" O2B DGT O 401 " pdb="MG MG O 402 " model vdw 2.188 2.170 nonbonded pdb=" O1A DGT O 401 " pdb="MG MG O 402 " model vdw 2.194 2.170 ... (remaining 706063 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and resid 6 through 84) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 4.760 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 157.170 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.239 68775 Z= 0.370 Angle : 0.848 24.394 93017 Z= 0.429 Chirality : 1.029 21.214 10122 Planarity : 0.006 0.105 11606 Dihedral : 14.908 176.039 26320 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.72 % Favored : 96.26 % Rotamer: Outliers : 0.01 % Allowed : 0.31 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.09), residues: 8031 helix: 0.57 (0.07), residues: 4432 sheet: -0.32 (0.26), residues: 396 loop : -0.57 (0.11), residues: 3203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 169 HIS 0.013 0.001 HIS a 27 PHE 0.062 0.002 PHE N 35 TYR 0.048 0.002 TYR A 104 ARG 0.012 0.000 ARG L 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1257 time to evaluate : 5.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 45 ASP cc_start: 0.9161 (m-30) cc_final: 0.8928 (m-30) REVERT: 6 112 LYS cc_start: 0.9283 (ttpp) cc_final: 0.8987 (ttmm) REVERT: 6 119 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8239 (tp30) REVERT: 1 324 GLN cc_start: 0.9368 (mm-40) cc_final: 0.9163 (mm-40) REVERT: 9 14 VAL cc_start: 0.8455 (t) cc_final: 0.8186 (p) REVERT: Q 14 ASP cc_start: 0.8925 (p0) cc_final: 0.8466 (p0) REVERT: 7 3 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8903 (mm-40) REVERT: T 19 LEU cc_start: 0.9373 (mm) cc_final: 0.9101 (mm) REVERT: T 26 ASP cc_start: 0.8546 (p0) cc_final: 0.8228 (p0) REVERT: T 35 HIS cc_start: 0.8539 (t-90) cc_final: 0.8234 (t-90) REVERT: T 43 ASP cc_start: 0.8849 (t0) cc_final: 0.8565 (t0) REVERT: T 52 MET cc_start: 0.8983 (mtm) cc_final: 0.8684 (mtm) REVERT: T 64 ASP cc_start: 0.8000 (t0) cc_final: 0.7734 (t0) REVERT: V 33 ILE cc_start: 0.9426 (tp) cc_final: 0.9162 (tp) REVERT: V 63 ASP cc_start: 0.9103 (t0) cc_final: 0.8619 (t0) REVERT: V 93 MET cc_start: 0.9546 (mmp) cc_final: 0.9236 (mmp) REVERT: W 59 LYS cc_start: 0.9201 (tptp) cc_final: 0.8805 (tmtm) REVERT: W 63 ASP cc_start: 0.9108 (m-30) cc_final: 0.8569 (m-30) REVERT: q 2 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8756 (mt-10) REVERT: A 109 LYS cc_start: 0.9602 (mtmt) cc_final: 0.9324 (mtmm) REVERT: H 183 MET cc_start: 0.9332 (mtp) cc_final: 0.9083 (mtm) REVERT: J 63 MET cc_start: 0.9229 (tpt) cc_final: 0.9023 (tpp) REVERT: J 122 ASP cc_start: 0.9363 (m-30) cc_final: 0.8928 (m-30) REVERT: J 125 MET cc_start: 0.9387 (mmm) cc_final: 0.9182 (mmm) REVERT: L 145 GLU cc_start: 0.9187 (mp0) cc_final: 0.8718 (mp0) REVERT: L 314 MET cc_start: 0.9611 (tpt) cc_final: 0.9391 (mmm) REVERT: M 281 ASP cc_start: 0.8508 (t0) cc_final: 0.8251 (t0) REVERT: O 192 MET cc_start: 0.9472 (mtm) cc_final: 0.9004 (mpt) REVERT: O 265 ASP cc_start: 0.8703 (t70) cc_final: 0.8259 (t0) REVERT: U 29 LYS cc_start: 0.9522 (mmmm) cc_final: 0.9153 (mmmm) REVERT: U 52 MET cc_start: 0.9367 (mtm) cc_final: 0.9114 (mtp) REVERT: X 108 GLN cc_start: 0.8940 (tp40) cc_final: 0.8598 (tp40) REVERT: Y 30 ILE cc_start: 0.9537 (mm) cc_final: 0.9315 (mp) REVERT: d 9 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8934 (mm-30) REVERT: g 46 ASP cc_start: 0.9201 (t70) cc_final: 0.8928 (t0) REVERT: g 56 MET cc_start: 0.9242 (tmm) cc_final: 0.9020 (tmm) REVERT: g 97 TYR cc_start: 0.9341 (t80) cc_final: 0.9117 (t80) REVERT: i 12 GLN cc_start: 0.9223 (mt0) cc_final: 0.8924 (mt0) REVERT: i 16 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8863 (tp30) REVERT: i 23 LYS cc_start: 0.9629 (tptm) cc_final: 0.9375 (tppp) REVERT: j 55 ASP cc_start: 0.9120 (t70) cc_final: 0.8340 (t0) REVERT: j 58 GLN cc_start: 0.9366 (mm110) cc_final: 0.9020 (mm-40) REVERT: k 29 ILE cc_start: 0.8667 (tp) cc_final: 0.8253 (tp) REVERT: m 61 ASP cc_start: 0.9160 (t70) cc_final: 0.8790 (t0) REVERT: m 112 GLU cc_start: 0.9480 (tp30) cc_final: 0.9051 (mm-30) REVERT: m 116 GLN cc_start: 0.9415 (mm110) cc_final: 0.8981 (mm110) REVERT: o 17 ASP cc_start: 0.8605 (p0) cc_final: 0.8325 (p0) REVERT: o 47 ASP cc_start: 0.9070 (m-30) cc_final: 0.8835 (m-30) REVERT: o 112 LYS cc_start: 0.9569 (tttm) cc_final: 0.9217 (ttpp) REVERT: o 116 LEU cc_start: 0.9274 (pp) cc_final: 0.9065 (pp) REVERT: p 72 ASP cc_start: 0.8148 (t0) cc_final: 0.7895 (t0) outliers start: 1 outliers final: 4 residues processed: 1257 average time/residue: 1.5206 time to fit residues: 2474.9766 Evaluate side-chains 998 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 994 time to evaluate : 5.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain n residue 122 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 7.9990 chunk 601 optimal weight: 20.0000 chunk 333 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 405 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 chunk 621 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 377 optimal weight: 7.9990 chunk 462 optimal weight: 5.9990 chunk 720 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 HIS C 200 ASN ** 1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 546 GLN P 181 HIS ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 288 HIS Q 46 GLN ** 7 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN W 60 GLN W 101 GLN q 13 GLN H 304 HIS J 107 ASN L 170 GLN L 572 ASN M 139 GLN M 399 ASN ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 142 HIS d 3 ASN d 59 HIS d 79 GLN ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 10 HIS h 108 GLN h 143 ASN i 127 HIS k 65 ASN m 51 ASN n 72 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 68775 Z= 0.546 Angle : 1.573 51.380 93017 Z= 1.018 Chirality : 0.308 6.441 10122 Planarity : 0.005 0.069 11606 Dihedral : 11.250 176.975 10199 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.14 % Favored : 96.85 % Rotamer: Outliers : 1.64 % Allowed : 10.27 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.09), residues: 8031 helix: 1.25 (0.08), residues: 4458 sheet: -0.26 (0.25), residues: 409 loop : -0.32 (0.11), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 326 HIS 0.008 0.001 HIS 9 67 PHE 0.030 0.001 PHE M 151 TYR 0.031 0.001 TYR L 422 ARG 0.013 0.000 ARG c 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1048 time to evaluate : 5.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 45 ASP cc_start: 0.9222 (m-30) cc_final: 0.8982 (m-30) REVERT: 6 119 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8256 (tp30) REVERT: D 47 MET cc_start: 0.8962 (mmm) cc_final: 0.8677 (tpp) REVERT: D 75 LYS cc_start: 0.9379 (tmmm) cc_final: 0.9145 (tmmm) REVERT: 3 35 MET cc_start: 0.9220 (tmt) cc_final: 0.9009 (tmt) REVERT: 3 440 CYS cc_start: 0.8813 (t) cc_final: 0.8611 (t) REVERT: 9 8 LYS cc_start: 0.8098 (pptt) cc_final: 0.7723 (pptt) REVERT: 9 14 VAL cc_start: 0.8477 (t) cc_final: 0.8200 (p) REVERT: 7 3 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8890 (mm-40) REVERT: S 88 ARG cc_start: 0.9125 (ptp-110) cc_final: 0.8914 (ptp-110) REVERT: T 35 HIS cc_start: 0.8580 (t-90) cc_final: 0.8254 (t-90) REVERT: T 52 MET cc_start: 0.8864 (mtm) cc_final: 0.8631 (mtm) REVERT: V 33 ILE cc_start: 0.9428 (tp) cc_final: 0.9224 (tp) REVERT: V 63 ASP cc_start: 0.9128 (t0) cc_final: 0.8724 (t0) REVERT: V 93 MET cc_start: 0.9589 (mmp) cc_final: 0.9387 (mmp) REVERT: V 104 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8543 (tm-30) REVERT: W 59 LYS cc_start: 0.9187 (tptp) cc_final: 0.8729 (tmtm) REVERT: W 63 ASP cc_start: 0.9050 (m-30) cc_final: 0.8400 (m-30) REVERT: q 1 MET cc_start: 0.8804 (ppp) cc_final: 0.8544 (ppp) REVERT: A 109 LYS cc_start: 0.9557 (mtmt) cc_final: 0.9216 (mmtm) REVERT: H 51 ASP cc_start: 0.9289 (m-30) cc_final: 0.9060 (m-30) REVERT: J 91 PHE cc_start: 0.8051 (m-80) cc_final: 0.7757 (m-80) REVERT: J 122 ASP cc_start: 0.9406 (m-30) cc_final: 0.8936 (m-30) REVERT: J 125 MET cc_start: 0.9403 (mmm) cc_final: 0.9119 (mmm) REVERT: J 136 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8685 (pp20) REVERT: K 57 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8747 (mmm) REVERT: K 88 ASP cc_start: 0.9285 (p0) cc_final: 0.9079 (p0) REVERT: L 145 GLU cc_start: 0.9187 (mp0) cc_final: 0.8667 (mp0) REVERT: L 267 THR cc_start: 0.9387 (m) cc_final: 0.9008 (p) REVERT: L 353 GLU cc_start: 0.9120 (tp30) cc_final: 0.8843 (tm-30) REVERT: M 87 ASP cc_start: 0.8532 (t0) cc_final: 0.8145 (t70) REVERT: M 281 ASP cc_start: 0.8659 (t0) cc_final: 0.8416 (t0) REVERT: M 307 TRP cc_start: 0.8666 (m100) cc_final: 0.8346 (m100) REVERT: O 192 MET cc_start: 0.9544 (mtm) cc_final: 0.9184 (mtm) REVERT: O 214 MET cc_start: 0.9136 (mmm) cc_final: 0.8934 (mmm) REVERT: O 242 LYS cc_start: 0.9189 (tppt) cc_final: 0.8976 (mmpt) REVERT: O 265 ASP cc_start: 0.8765 (t70) cc_final: 0.8329 (t0) REVERT: U 29 LYS cc_start: 0.9528 (mmmm) cc_final: 0.9111 (mmmm) REVERT: U 37 MET cc_start: 0.9078 (mpt) cc_final: 0.8835 (mpt) REVERT: X 108 GLN cc_start: 0.8937 (tp40) cc_final: 0.8704 (tp40) REVERT: X 112 ASP cc_start: 0.8894 (m-30) cc_final: 0.8661 (m-30) REVERT: Y 30 ILE cc_start: 0.9564 (mm) cc_final: 0.9344 (mp) REVERT: Y 85 ASP cc_start: 0.9254 (t0) cc_final: 0.8850 (t0) REVERT: Y 87 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9238 (tm) REVERT: Z 6 LYS cc_start: 0.9167 (tppt) cc_final: 0.8909 (tptm) REVERT: d 9 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8976 (mm-30) REVERT: d 27 ASN cc_start: 0.7776 (p0) cc_final: 0.7522 (p0) REVERT: f 45 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8306 (tp40) REVERT: f 52 GLU cc_start: 0.8810 (pt0) cc_final: 0.8589 (pt0) REVERT: g 46 ASP cc_start: 0.9233 (t70) cc_final: 0.8932 (t0) REVERT: i 12 GLN cc_start: 0.9208 (mt0) cc_final: 0.8913 (mt0) REVERT: i 16 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8800 (tp30) REVERT: i 23 LYS cc_start: 0.9639 (tptm) cc_final: 0.9386 (tppp) REVERT: j 43 ASP cc_start: 0.8900 (p0) cc_final: 0.8693 (p0) REVERT: j 55 ASP cc_start: 0.9062 (t70) cc_final: 0.8417 (t0) REVERT: j 58 GLN cc_start: 0.9384 (mm110) cc_final: 0.9062 (mm-40) REVERT: m 61 ASP cc_start: 0.9156 (t70) cc_final: 0.8823 (t0) REVERT: m 112 GLU cc_start: 0.9486 (tp30) cc_final: 0.9230 (mm-30) REVERT: m 117 GLU cc_start: 0.9164 (pm20) cc_final: 0.8812 (pm20) REVERT: o 17 ASP cc_start: 0.8596 (p0) cc_final: 0.7751 (p0) REVERT: o 47 ASP cc_start: 0.9141 (m-30) cc_final: 0.8938 (m-30) REVERT: p 37 ASP cc_start: 0.9152 (m-30) cc_final: 0.8924 (m-30) REVERT: p 58 ASN cc_start: 0.8142 (m110) cc_final: 0.7875 (m-40) outliers start: 117 outliers final: 41 residues processed: 1084 average time/residue: 1.4930 time to fit residues: 2111.7214 Evaluate side-chains 1036 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 992 time to evaluate : 5.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 59 THR Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 9 residue 38 MET Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain T residue 33 ASN Chi-restraints excluded: chain V residue 17 ASP Chi-restraints excluded: chain W residue 97 LYS Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 133 ASP Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 106 SER Chi-restraints excluded: chain Z residue 19 ASP Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 76 ILE Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 80 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 599 optimal weight: 20.0000 chunk 490 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 721 optimal weight: 7.9990 chunk 779 optimal weight: 20.0000 chunk 642 optimal weight: 9.9990 chunk 715 optimal weight: 20.0000 chunk 245 optimal weight: 0.0370 chunk 578 optimal weight: 5.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 257 ASN 1 437 HIS ** 3 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 203 GLN P 250 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 ASN O 141 GLN O 200 GLN d 3 ASN ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 108 GLN l 86 ASN m 51 ASN o 53 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.275 68775 Z= 0.543 Angle : 1.564 50.937 93017 Z= 1.013 Chirality : 0.311 6.528 10122 Planarity : 0.004 0.062 11606 Dihedral : 10.631 175.293 10190 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.29 % Favored : 96.70 % Rotamer: Outliers : 2.06 % Allowed : 11.53 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.10), residues: 8031 helix: 1.52 (0.08), residues: 4446 sheet: -0.24 (0.25), residues: 412 loop : -0.17 (0.11), residues: 3173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP P 326 HIS 0.008 0.001 HIS 9 67 PHE 0.029 0.001 PHE M 151 TYR 0.025 0.001 TYR J 108 ARG 0.009 0.000 ARG m 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1045 time to evaluate : 5.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 45 ASP cc_start: 0.9192 (m-30) cc_final: 0.8965 (m-30) REVERT: 6 119 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8226 (tp30) REVERT: 1 317 MET cc_start: 0.9353 (mmt) cc_final: 0.8902 (mmt) REVERT: 3 35 MET cc_start: 0.9189 (tmt) cc_final: 0.8985 (tmt) REVERT: 9 8 LYS cc_start: 0.8063 (pptt) cc_final: 0.7512 (pptt) REVERT: 9 14 VAL cc_start: 0.8506 (t) cc_final: 0.8233 (p) REVERT: Q 14 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8219 (p0) REVERT: 7 3 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8882 (mm-40) REVERT: 7 51 GLU cc_start: 0.8804 (tp30) cc_final: 0.8504 (tp30) REVERT: T 12 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8976 (tmmm) REVERT: T 35 HIS cc_start: 0.8729 (t-90) cc_final: 0.8339 (t-90) REVERT: T 52 MET cc_start: 0.8874 (mtm) cc_final: 0.8612 (mtm) REVERT: V 33 ILE cc_start: 0.9437 (tp) cc_final: 0.9179 (tp) REVERT: V 63 ASP cc_start: 0.9141 (t0) cc_final: 0.8767 (t0) REVERT: W 59 LYS cc_start: 0.9214 (tptp) cc_final: 0.8732 (tmtm) REVERT: W 63 ASP cc_start: 0.9026 (m-30) cc_final: 0.8383 (m-30) REVERT: q 1 MET cc_start: 0.8699 (ppp) cc_final: 0.8367 (ppp) REVERT: A 109 LYS cc_start: 0.9534 (mtmt) cc_final: 0.9291 (mmtm) REVERT: H 51 ASP cc_start: 0.9316 (m-30) cc_final: 0.9097 (m-30) REVERT: J 67 PHE cc_start: 0.9730 (m-80) cc_final: 0.9525 (m-80) REVERT: J 91 PHE cc_start: 0.8092 (m-80) cc_final: 0.7724 (m-80) REVERT: J 122 ASP cc_start: 0.9404 (m-30) cc_final: 0.8936 (m-30) REVERT: J 125 MET cc_start: 0.9397 (mmm) cc_final: 0.9146 (mmm) REVERT: K 57 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8793 (mmm) REVERT: K 88 ASP cc_start: 0.9311 (p0) cc_final: 0.9054 (p0) REVERT: L 145 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: L 267 THR cc_start: 0.9394 (m) cc_final: 0.9048 (p) REVERT: M 87 ASP cc_start: 0.8601 (t0) cc_final: 0.8197 (t70) REVERT: M 114 GLU cc_start: 0.8993 (tp30) cc_final: 0.8702 (tp30) REVERT: M 281 ASP cc_start: 0.8771 (t0) cc_final: 0.8500 (t0) REVERT: M 307 TRP cc_start: 0.8901 (m100) cc_final: 0.8463 (m100) REVERT: N 117 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8074 (mm-30) REVERT: O 265 ASP cc_start: 0.8838 (t70) cc_final: 0.8422 (t0) REVERT: X 89 ASP cc_start: 0.9478 (t70) cc_final: 0.9154 (t0) REVERT: X 108 GLN cc_start: 0.8948 (tp40) cc_final: 0.8695 (tp40) REVERT: Y 30 ILE cc_start: 0.9564 (mm) cc_final: 0.9358 (mp) REVERT: Z 6 LYS cc_start: 0.9247 (tppt) cc_final: 0.8987 (tptm) REVERT: c 37 GLU cc_start: 0.9375 (tp30) cc_final: 0.8909 (tm-30) REVERT: d 9 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8981 (mm-30) REVERT: g 46 ASP cc_start: 0.9170 (t70) cc_final: 0.8671 (t70) REVERT: g 84 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8490 (mm-40) REVERT: i 12 GLN cc_start: 0.9206 (mt0) cc_final: 0.8903 (mt0) REVERT: i 16 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8795 (tp30) REVERT: i 23 LYS cc_start: 0.9618 (tptm) cc_final: 0.9361 (tppp) REVERT: i 92 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9121 (mppt) REVERT: j 13 GLU cc_start: 0.9542 (OUTLIER) cc_final: 0.9116 (mp0) REVERT: j 43 ASP cc_start: 0.8837 (p0) cc_final: 0.8613 (p0) REVERT: j 55 ASP cc_start: 0.9043 (t70) cc_final: 0.8399 (t0) REVERT: j 58 GLN cc_start: 0.9360 (mm110) cc_final: 0.9060 (mm-40) REVERT: l 67 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.8717 (tm-30) REVERT: l 148 GLU cc_start: 0.9244 (tp30) cc_final: 0.8982 (tp30) REVERT: m 61 ASP cc_start: 0.9193 (t70) cc_final: 0.8880 (t0) REVERT: m 112 GLU cc_start: 0.9490 (tp30) cc_final: 0.9210 (mm-30) REVERT: n 52 ASN cc_start: 0.8651 (m-40) cc_final: 0.8345 (m-40) REVERT: p 37 ASP cc_start: 0.9104 (m-30) cc_final: 0.8852 (m-30) REVERT: p 58 ASN cc_start: 0.8373 (m110) cc_final: 0.8167 (m110) outliers start: 147 outliers final: 60 residues processed: 1088 average time/residue: 1.4607 time to fit residues: 2092.2518 Evaluate side-chains 1058 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 990 time to evaluate : 5.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 59 THR Chi-restraints excluded: chain 6 residue 60 PHE Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain W residue 67 GLU Chi-restraints excluded: chain W residue 97 LYS Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 314 MET Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain X residue 133 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Y residue 106 SER Chi-restraints excluded: chain Z residue 19 ASP Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 84 GLN Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 76 ILE Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 80 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 8.9990 chunk 542 optimal weight: 20.0000 chunk 374 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 344 optimal weight: 30.0000 chunk 484 optimal weight: 7.9990 chunk 724 optimal weight: 8.9990 chunk 766 optimal weight: 30.0000 chunk 378 optimal weight: 20.0000 chunk 686 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN ** 3 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 250 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN ** r 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN J 107 ASN L 56 HIS M 51 ASN ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 10 ASN d 3 ASN ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 108 GLN m 51 ASN n 72 GLN o 53 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.272 68775 Z= 0.561 Angle : 1.571 50.967 93017 Z= 1.016 Chirality : 0.311 6.525 10122 Planarity : 0.004 0.059 11606 Dihedral : 10.307 174.343 10190 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.41 % Favored : 96.58 % Rotamer: Outliers : 2.18 % Allowed : 12.99 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.10), residues: 8031 helix: 1.64 (0.08), residues: 4422 sheet: -0.21 (0.24), residues: 445 loop : -0.07 (0.12), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP P 326 HIS 0.008 0.001 HIS 9 67 PHE 0.040 0.001 PHE l 1 TYR 0.028 0.001 TYR A 104 ARG 0.015 0.000 ARG c 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1028 time to evaluate : 5.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 112 LYS cc_start: 0.9347 (ttmm) cc_final: 0.9107 (ttpp) REVERT: 9 14 VAL cc_start: 0.8693 (t) cc_final: 0.8453 (p) REVERT: Q 28 GLU cc_start: 0.9149 (tt0) cc_final: 0.8893 (tm-30) REVERT: 7 3 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8886 (mm-40) REVERT: 7 51 GLU cc_start: 0.8827 (tp30) cc_final: 0.8499 (tp30) REVERT: T 35 HIS cc_start: 0.8693 (t-90) cc_final: 0.8348 (t-90) REVERT: T 52 MET cc_start: 0.8910 (mtm) cc_final: 0.8693 (mtm) REVERT: T 84 LYS cc_start: 0.8811 (mttt) cc_final: 0.8524 (mmmm) REVERT: V 33 ILE cc_start: 0.9454 (tp) cc_final: 0.9190 (tp) REVERT: V 63 ASP cc_start: 0.9163 (t0) cc_final: 0.8819 (t0) REVERT: W 59 LYS cc_start: 0.9266 (tptp) cc_final: 0.8798 (tmtm) REVERT: W 63 ASP cc_start: 0.9021 (m-30) cc_final: 0.8427 (m-30) REVERT: q 1 MET cc_start: 0.8722 (ppp) cc_final: 0.8329 (ppp) REVERT: A 109 LYS cc_start: 0.9551 (mtmt) cc_final: 0.9273 (mmtm) REVERT: H 51 ASP cc_start: 0.9329 (m-30) cc_final: 0.9122 (m-30) REVERT: J 63 MET cc_start: 0.9387 (tpt) cc_final: 0.9134 (tpp) REVERT: J 91 PHE cc_start: 0.8048 (m-80) cc_final: 0.7593 (m-80) REVERT: J 122 ASP cc_start: 0.9410 (m-30) cc_final: 0.8942 (m-30) REVERT: J 125 MET cc_start: 0.9382 (mmm) cc_final: 0.9113 (mmm) REVERT: J 152 MET cc_start: 0.9535 (tpp) cc_final: 0.9287 (tpp) REVERT: K 88 ASP cc_start: 0.9346 (p0) cc_final: 0.9044 (p0) REVERT: L 145 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.8710 (mp0) REVERT: L 267 THR cc_start: 0.9457 (m) cc_final: 0.9111 (p) REVERT: L 476 SER cc_start: 0.8390 (m) cc_final: 0.8141 (t) REVERT: L 539 MET cc_start: 0.9454 (tmm) cc_final: 0.9190 (tmm) REVERT: L 562 ILE cc_start: 0.9450 (mp) cc_final: 0.9245 (mp) REVERT: M 87 ASP cc_start: 0.8671 (t0) cc_final: 0.8282 (t70) REVERT: M 281 ASP cc_start: 0.8892 (t0) cc_final: 0.8609 (t0) REVERT: M 307 TRP cc_start: 0.9020 (m100) cc_final: 0.8706 (m100) REVERT: N 117 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8179 (mm-30) REVERT: N 139 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9156 (mt) REVERT: O 265 ASP cc_start: 0.8830 (t70) cc_final: 0.8463 (t0) REVERT: X 89 ASP cc_start: 0.9519 (t70) cc_final: 0.9187 (t0) REVERT: Y 2 LYS cc_start: 0.8959 (mppt) cc_final: 0.8449 (mmtp) REVERT: Y 30 ILE cc_start: 0.9576 (mm) cc_final: 0.9365 (mp) REVERT: Z 129 LYS cc_start: 0.9511 (ptmt) cc_final: 0.9136 (ttpp) REVERT: a 43 TYR cc_start: 0.9511 (t80) cc_final: 0.9282 (t80) REVERT: c 6 GLU cc_start: 0.8924 (tp30) cc_final: 0.8605 (tp30) REVERT: c 37 GLU cc_start: 0.9376 (tp30) cc_final: 0.8838 (tm-30) REVERT: d 9 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8963 (mm-30) REVERT: d 25 LYS cc_start: 0.8993 (ttpm) cc_final: 0.8600 (ptmm) REVERT: d 104 LYS cc_start: 0.9053 (ptmm) cc_final: 0.8614 (ttpp) REVERT: g 46 ASP cc_start: 0.9151 (t70) cc_final: 0.8671 (t70) REVERT: i 12 GLN cc_start: 0.9208 (mt0) cc_final: 0.8899 (mt0) REVERT: i 16 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8818 (tp30) REVERT: i 23 LYS cc_start: 0.9621 (tptm) cc_final: 0.9370 (tppp) REVERT: i 92 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9119 (mppt) REVERT: j 13 GLU cc_start: 0.9551 (OUTLIER) cc_final: 0.9176 (mp0) REVERT: j 43 ASP cc_start: 0.8746 (p0) cc_final: 0.8542 (p0) REVERT: j 55 ASP cc_start: 0.9046 (t70) cc_final: 0.8459 (t0) REVERT: j 58 GLN cc_start: 0.9386 (mm110) cc_final: 0.9062 (mm-40) REVERT: l 148 GLU cc_start: 0.9230 (tp30) cc_final: 0.8860 (tp30) REVERT: m 61 ASP cc_start: 0.9265 (t70) cc_final: 0.8987 (t0) REVERT: m 112 GLU cc_start: 0.9497 (tp30) cc_final: 0.9274 (mm-30) REVERT: n 52 ASN cc_start: 0.8731 (m-40) cc_final: 0.8265 (m-40) REVERT: o 17 ASP cc_start: 0.8493 (p0) cc_final: 0.8248 (p0) REVERT: p 37 ASP cc_start: 0.9099 (m-30) cc_final: 0.8830 (m-30) REVERT: p 80 ASP cc_start: 0.9042 (t0) cc_final: 0.8793 (t0) outliers start: 156 outliers final: 64 residues processed: 1087 average time/residue: 1.4869 time to fit residues: 2110.6903 Evaluate side-chains 1047 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 979 time to evaluate : 5.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 59 THR Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain W residue 97 LYS Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain r residue 107 LYS Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain L residue 71 MET Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain X residue 93 MET Chi-restraints excluded: chain X residue 133 ASP Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Y residue 106 SER Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 117 GLU Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 0.9990 chunk 435 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 570 optimal weight: 9.9990 chunk 316 optimal weight: 9.9990 chunk 654 optimal weight: 20.0000 chunk 529 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 391 optimal weight: 4.9990 chunk 688 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 250 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN ** r 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN H 47 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN J 2 ASN J 107 ASN ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 3 ASN ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 24 GLN m 49 GLN m 51 ASN o 43 GLN o 53 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.270 68775 Z= 0.545 Angle : 1.567 50.921 93017 Z= 1.014 Chirality : 0.310 6.511 10122 Planarity : 0.004 0.061 11606 Dihedral : 10.136 174.502 10190 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer: Outliers : 1.97 % Allowed : 14.41 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.10), residues: 8031 helix: 1.70 (0.08), residues: 4410 sheet: -0.11 (0.24), residues: 432 loop : -0.06 (0.11), residues: 3189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP P 326 HIS 0.007 0.001 HIS 9 67 PHE 0.031 0.001 PHE l 1 TYR 0.032 0.001 TYR N 146 ARG 0.009 0.000 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1023 time to evaluate : 5.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 112 LYS cc_start: 0.9341 (ttmm) cc_final: 0.9109 (ttpp) REVERT: 3 35 MET cc_start: 0.9182 (tmt) cc_final: 0.8911 (tmt) REVERT: 9 14 VAL cc_start: 0.8710 (t) cc_final: 0.8480 (p) REVERT: P 196 LEU cc_start: 0.8422 (tp) cc_final: 0.8220 (tp) REVERT: Q 28 GLU cc_start: 0.9143 (tt0) cc_final: 0.8867 (tm-30) REVERT: 7 3 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8927 (mm-40) REVERT: 7 51 GLU cc_start: 0.8805 (tp30) cc_final: 0.8458 (tp30) REVERT: T 19 LEU cc_start: 0.9526 (mm) cc_final: 0.9299 (mm) REVERT: T 20 LYS cc_start: 0.9354 (mmmt) cc_final: 0.9072 (mmmt) REVERT: T 35 HIS cc_start: 0.8724 (t-90) cc_final: 0.8373 (t-90) REVERT: T 47 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8872 (tm-30) REVERT: T 52 MET cc_start: 0.8926 (mtm) cc_final: 0.8711 (mtm) REVERT: T 84 LYS cc_start: 0.8997 (mttt) cc_final: 0.8699 (mmmm) REVERT: V 33 ILE cc_start: 0.9446 (tp) cc_final: 0.9176 (tp) REVERT: V 63 ASP cc_start: 0.9172 (t0) cc_final: 0.8836 (t0) REVERT: W 59 LYS cc_start: 0.9266 (tptp) cc_final: 0.8792 (tmtm) REVERT: W 63 ASP cc_start: 0.9013 (m-30) cc_final: 0.8438 (m-30) REVERT: q 1 MET cc_start: 0.8723 (ppp) cc_final: 0.8251 (ppp) REVERT: A 109 LYS cc_start: 0.9515 (mtmt) cc_final: 0.9313 (mmtm) REVERT: H 51 ASP cc_start: 0.9357 (m-30) cc_final: 0.9151 (m-30) REVERT: J 63 MET cc_start: 0.9362 (tpt) cc_final: 0.9104 (tpp) REVERT: J 91 PHE cc_start: 0.8073 (m-80) cc_final: 0.7806 (m-80) REVERT: J 122 ASP cc_start: 0.9403 (m-30) cc_final: 0.8948 (m-30) REVERT: J 125 MET cc_start: 0.9365 (mmm) cc_final: 0.9095 (mmm) REVERT: J 152 MET cc_start: 0.9474 (tpp) cc_final: 0.9143 (tpp) REVERT: K 88 ASP cc_start: 0.9360 (p0) cc_final: 0.9077 (p0) REVERT: L 145 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8700 (mp0) REVERT: L 267 THR cc_start: 0.9454 (m) cc_final: 0.9167 (p) REVERT: L 476 SER cc_start: 0.8419 (m) cc_final: 0.8132 (t) REVERT: L 539 MET cc_start: 0.9482 (tmm) cc_final: 0.9204 (tmm) REVERT: L 559 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8928 (tp30) REVERT: M 87 ASP cc_start: 0.8681 (t0) cc_final: 0.8243 (t70) REVERT: M 114 GLU cc_start: 0.9041 (tp30) cc_final: 0.8662 (tp30) REVERT: M 123 GLU cc_start: 0.9201 (mp0) cc_final: 0.8706 (mp0) REVERT: M 281 ASP cc_start: 0.8901 (t0) cc_final: 0.8605 (t0) REVERT: M 307 TRP cc_start: 0.8917 (m100) cc_final: 0.8492 (m100) REVERT: M 310 MET cc_start: 0.9288 (tmm) cc_final: 0.8111 (ttm) REVERT: N 97 MET cc_start: 0.9544 (OUTLIER) cc_final: 0.9149 (mmt) REVERT: N 117 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8183 (mm-30) REVERT: N 139 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9153 (mt) REVERT: O 265 ASP cc_start: 0.8820 (t70) cc_final: 0.8459 (t0) REVERT: U 37 MET cc_start: 0.9229 (mpt) cc_final: 0.8760 (mpt) REVERT: X 89 ASP cc_start: 0.9523 (t70) cc_final: 0.9204 (t0) REVERT: Y 2 LYS cc_start: 0.8969 (mppt) cc_final: 0.8721 (mmtp) REVERT: Y 30 ILE cc_start: 0.9573 (mm) cc_final: 0.9364 (mp) REVERT: Z 129 LYS cc_start: 0.9519 (ptmt) cc_final: 0.9142 (ttpp) REVERT: a 43 TYR cc_start: 0.9528 (t80) cc_final: 0.9289 (t80) REVERT: c 6 GLU cc_start: 0.8970 (tp30) cc_final: 0.8643 (tp30) REVERT: c 37 GLU cc_start: 0.9378 (tp30) cc_final: 0.8814 (tm-30) REVERT: d 9 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8959 (mm-30) REVERT: e 4 ASP cc_start: 0.8890 (m-30) cc_final: 0.8585 (m-30) REVERT: g 46 ASP cc_start: 0.9128 (t70) cc_final: 0.8614 (t70) REVERT: i 12 GLN cc_start: 0.9208 (mt0) cc_final: 0.8903 (mt0) REVERT: i 16 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8816 (tp30) REVERT: i 23 LYS cc_start: 0.9619 (tptm) cc_final: 0.9358 (tppp) REVERT: i 92 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9089 (mppt) REVERT: j 13 GLU cc_start: 0.9570 (OUTLIER) cc_final: 0.9197 (mp0) REVERT: j 55 ASP cc_start: 0.9012 (t70) cc_final: 0.8423 (t0) REVERT: j 58 GLN cc_start: 0.9373 (mm110) cc_final: 0.9059 (mm-40) REVERT: l 148 GLU cc_start: 0.9243 (tp30) cc_final: 0.8961 (tp30) REVERT: m 54 LYS cc_start: 0.9477 (mmpt) cc_final: 0.9131 (mmpt) REVERT: m 61 ASP cc_start: 0.9252 (t70) cc_final: 0.8977 (t0) REVERT: m 107 ASP cc_start: 0.9476 (t0) cc_final: 0.9134 (t0) REVERT: m 112 GLU cc_start: 0.9479 (tp30) cc_final: 0.9265 (mm-30) REVERT: n 52 ASN cc_start: 0.8776 (m-40) cc_final: 0.8330 (m-40) REVERT: o 17 ASP cc_start: 0.8338 (p0) cc_final: 0.7157 (p0) REVERT: o 20 LYS cc_start: 0.9042 (pmtt) cc_final: 0.8750 (pmtt) REVERT: p 37 ASP cc_start: 0.9087 (m-30) cc_final: 0.8817 (m-30) REVERT: p 80 ASP cc_start: 0.9039 (t0) cc_final: 0.8765 (t0) outliers start: 141 outliers final: 67 residues processed: 1081 average time/residue: 1.5092 time to fit residues: 2128.1633 Evaluate side-chains 1050 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 978 time to evaluate : 5.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 59 THR Chi-restraints excluded: chain 6 residue 60 PHE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 326 TRP Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain W residue 97 LYS Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain X residue 93 MET Chi-restraints excluded: chain X residue 133 ASP Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Z residue 19 ASP Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain Z residue 143 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 58 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 9.9990 chunk 690 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 450 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 767 optimal weight: 30.0000 chunk 636 optimal weight: 7.9990 chunk 355 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 253 optimal weight: 20.0000 chunk 402 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 459 GLN P 250 HIS Q 43 ASN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN W 101 GLN ** r 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN J 2 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 ASN M 399 ASN ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 174 GLN O 180 GLN ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN m 51 ASN n 72 GLN o 53 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.272 68775 Z= 0.602 Angle : 1.587 50.990 93017 Z= 1.022 Chirality : 0.311 6.531 10122 Planarity : 0.004 0.061 11606 Dihedral : 10.129 173.273 10190 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.60 % Favored : 96.39 % Rotamer: Outliers : 2.31 % Allowed : 15.02 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.10), residues: 8031 helix: 1.70 (0.08), residues: 4409 sheet: -0.11 (0.24), residues: 434 loop : -0.02 (0.12), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP P 326 HIS 0.009 0.001 HIS 9 67 PHE 0.032 0.002 PHE l 1 TYR 0.036 0.001 TYR N 146 ARG 0.013 0.000 ARG c 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1002 time to evaluate : 5.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 44 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8791 (m-30) REVERT: 6 112 LYS cc_start: 0.9365 (ttmm) cc_final: 0.9132 (ttpp) REVERT: 6 119 GLU cc_start: 0.8681 (tp30) cc_final: 0.8315 (tp30) REVERT: 9 14 VAL cc_start: 0.8718 (t) cc_final: 0.8505 (p) REVERT: Q 16 LYS cc_start: 0.9073 (mppt) cc_final: 0.8461 (ttpp) REVERT: Q 28 GLU cc_start: 0.9193 (tt0) cc_final: 0.8931 (tm-30) REVERT: 7 51 GLU cc_start: 0.8825 (tp30) cc_final: 0.8432 (tp30) REVERT: T 35 HIS cc_start: 0.8721 (t-90) cc_final: 0.8358 (t-90) REVERT: T 47 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8931 (tm-30) REVERT: T 52 MET cc_start: 0.8942 (mtm) cc_final: 0.8740 (mtm) REVERT: V 33 ILE cc_start: 0.9461 (tp) cc_final: 0.9200 (tp) REVERT: V 63 ASP cc_start: 0.9200 (t0) cc_final: 0.8862 (t0) REVERT: W 59 LYS cc_start: 0.9276 (tptp) cc_final: 0.8762 (tmtm) REVERT: W 63 ASP cc_start: 0.9006 (m-30) cc_final: 0.8470 (m-30) REVERT: r 104 GLU cc_start: 0.9056 (pm20) cc_final: 0.8834 (pm20) REVERT: H 51 ASP cc_start: 0.9356 (m-30) cc_final: 0.9153 (m-30) REVERT: H 59 GLU cc_start: 0.8273 (pp20) cc_final: 0.7950 (pp20) REVERT: H 108 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8613 (p) REVERT: J 63 MET cc_start: 0.9415 (tpt) cc_final: 0.9198 (tpp) REVERT: J 91 PHE cc_start: 0.8124 (m-80) cc_final: 0.7829 (m-80) REVERT: J 122 ASP cc_start: 0.9431 (m-30) cc_final: 0.8954 (m-30) REVERT: J 125 MET cc_start: 0.9357 (mmm) cc_final: 0.9079 (mmm) REVERT: K 88 ASP cc_start: 0.9373 (p0) cc_final: 0.9058 (p0) REVERT: L 145 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8709 (mp0) REVERT: L 267 THR cc_start: 0.9470 (m) cc_final: 0.9194 (p) REVERT: L 476 SER cc_start: 0.8489 (m) cc_final: 0.8169 (t) REVERT: L 539 MET cc_start: 0.9472 (tmm) cc_final: 0.9209 (tmm) REVERT: L 559 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8898 (tp30) REVERT: M 87 ASP cc_start: 0.8725 (t0) cc_final: 0.8291 (t70) REVERT: M 123 GLU cc_start: 0.9218 (mp0) cc_final: 0.8864 (mp0) REVERT: M 281 ASP cc_start: 0.8954 (t0) cc_final: 0.8721 (t0) REVERT: M 307 TRP cc_start: 0.9025 (m100) cc_final: 0.8580 (m100) REVERT: N 97 MET cc_start: 0.9551 (OUTLIER) cc_final: 0.9103 (tpt) REVERT: N 117 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8152 (mm-30) REVERT: N 139 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9108 (mm) REVERT: O 265 ASP cc_start: 0.8867 (t70) cc_final: 0.8492 (t0) REVERT: U 37 MET cc_start: 0.9265 (mpt) cc_final: 0.8688 (mpt) REVERT: U 49 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8779 (mt-10) REVERT: X 89 ASP cc_start: 0.9551 (t70) cc_final: 0.9227 (t0) REVERT: Y 2 LYS cc_start: 0.9012 (mppt) cc_final: 0.8693 (mmtp) REVERT: Y 30 ILE cc_start: 0.9586 (mm) cc_final: 0.9336 (mp) REVERT: Y 90 PHE cc_start: 0.9172 (t80) cc_final: 0.8917 (t80) REVERT: c 6 GLU cc_start: 0.8993 (tp30) cc_final: 0.8705 (tp30) REVERT: c 37 GLU cc_start: 0.9393 (tp30) cc_final: 0.8791 (tm-30) REVERT: d 9 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8968 (mm-30) REVERT: d 104 LYS cc_start: 0.9112 (ptmm) cc_final: 0.8673 (ttpp) REVERT: i 12 GLN cc_start: 0.9208 (mt0) cc_final: 0.8896 (mt0) REVERT: i 16 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8817 (tp30) REVERT: i 23 LYS cc_start: 0.9631 (tptm) cc_final: 0.9360 (tppp) REVERT: i 92 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9104 (mppt) REVERT: i 121 ASP cc_start: 0.8679 (m-30) cc_final: 0.8318 (p0) REVERT: j 13 GLU cc_start: 0.9580 (OUTLIER) cc_final: 0.9339 (mp0) REVERT: j 55 ASP cc_start: 0.9000 (t70) cc_final: 0.8426 (t0) REVERT: j 58 GLN cc_start: 0.9386 (mm110) cc_final: 0.9048 (mm-40) REVERT: m 27 GLU cc_start: 0.9392 (pm20) cc_final: 0.9113 (pm20) REVERT: m 61 ASP cc_start: 0.9280 (t70) cc_final: 0.9024 (t0) REVERT: n 52 ASN cc_start: 0.8904 (m-40) cc_final: 0.8513 (m-40) REVERT: o 20 LYS cc_start: 0.9153 (pmtt) cc_final: 0.8861 (ptpp) REVERT: o 104 GLU cc_start: 0.9240 (tm-30) cc_final: 0.9026 (tp30) REVERT: p 37 ASP cc_start: 0.9097 (m-30) cc_final: 0.8822 (m-30) REVERT: p 80 ASP cc_start: 0.9011 (t0) cc_final: 0.8660 (t0) outliers start: 165 outliers final: 85 residues processed: 1081 average time/residue: 1.4997 time to fit residues: 2115.8270 Evaluate side-chains 1064 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 971 time to evaluate : 5.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 44 ASP Chi-restraints excluded: chain 6 residue 59 THR Chi-restraints excluded: chain 6 residue 60 PHE Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 326 TRP Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain V residue 17 ASP Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain W residue 67 GLU Chi-restraints excluded: chain W residue 97 LYS Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain r residue 39 LYS Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain X residue 93 MET Chi-restraints excluded: chain X residue 133 ASP Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Y residue 106 SER Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 10 ASN Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 117 GLU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 58 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 437 optimal weight: 7.9990 chunk 560 optimal weight: 5.9990 chunk 434 optimal weight: 5.9990 chunk 645 optimal weight: 0.0170 chunk 428 optimal weight: 20.0000 chunk 764 optimal weight: 20.0000 chunk 478 optimal weight: 5.9990 chunk 465 optimal weight: 10.0000 chunk 352 optimal weight: 4.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN P 250 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN J 2 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 3 ASN ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 ASN m 49 GLN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.270 68775 Z= 0.549 Angle : 1.576 50.892 93017 Z= 1.017 Chirality : 0.310 6.503 10122 Planarity : 0.004 0.061 11606 Dihedral : 10.015 173.917 10190 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.40 % Favored : 96.59 % Rotamer: Outliers : 1.89 % Allowed : 16.03 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.10), residues: 8031 helix: 1.74 (0.08), residues: 4395 sheet: -0.08 (0.25), residues: 432 loop : -0.01 (0.12), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP P 326 HIS 0.007 0.001 HIS 9 67 PHE 0.027 0.001 PHE M 151 TYR 0.039 0.001 TYR N 146 ARG 0.011 0.000 ARG m 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1007 time to evaluate : 5.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 44 ASP cc_start: 0.9221 (OUTLIER) cc_final: 0.8782 (m-30) REVERT: 6 112 LYS cc_start: 0.9349 (ttmm) cc_final: 0.9123 (ttpp) REVERT: 6 119 GLU cc_start: 0.8656 (tp30) cc_final: 0.8322 (tp30) REVERT: 9 14 VAL cc_start: 0.8729 (t) cc_final: 0.8525 (p) REVERT: Q 28 GLU cc_start: 0.9179 (tt0) cc_final: 0.8921 (tm-30) REVERT: 7 51 GLU cc_start: 0.8853 (tp30) cc_final: 0.8454 (tp30) REVERT: T 35 HIS cc_start: 0.8778 (t-90) cc_final: 0.8439 (t-90) REVERT: T 47 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8892 (tm-30) REVERT: T 84 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8623 (mmmm) REVERT: V 33 ILE cc_start: 0.9437 (tp) cc_final: 0.9202 (tp) REVERT: V 63 ASP cc_start: 0.9206 (t0) cc_final: 0.8877 (t0) REVERT: W 59 LYS cc_start: 0.9261 (tptp) cc_final: 0.8741 (tmtm) REVERT: W 63 ASP cc_start: 0.9005 (m-30) cc_final: 0.8458 (m-30) REVERT: H 51 ASP cc_start: 0.9362 (m-30) cc_final: 0.9159 (m-30) REVERT: H 59 GLU cc_start: 0.8260 (pp20) cc_final: 0.7996 (pp20) REVERT: J 63 MET cc_start: 0.9405 (tpt) cc_final: 0.9195 (tpp) REVERT: J 69 TYR cc_start: 0.9277 (t80) cc_final: 0.9068 (t80) REVERT: J 91 PHE cc_start: 0.8114 (m-80) cc_final: 0.7821 (m-80) REVERT: J 122 ASP cc_start: 0.9417 (m-30) cc_final: 0.8940 (m-30) REVERT: J 125 MET cc_start: 0.9333 (mmm) cc_final: 0.9056 (mmm) REVERT: K 88 ASP cc_start: 0.9366 (p0) cc_final: 0.9072 (p0) REVERT: L 145 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: L 267 THR cc_start: 0.9475 (m) cc_final: 0.9227 (p) REVERT: L 476 SER cc_start: 0.8496 (m) cc_final: 0.8156 (t) REVERT: L 539 MET cc_start: 0.9487 (tmm) cc_final: 0.9209 (tmm) REVERT: L 559 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8814 (tp30) REVERT: M 87 ASP cc_start: 0.8702 (t0) cc_final: 0.8284 (t70) REVERT: M 114 GLU cc_start: 0.8910 (tp30) cc_final: 0.8613 (tp30) REVERT: M 123 GLU cc_start: 0.9216 (mp0) cc_final: 0.8850 (mp0) REVERT: M 281 ASP cc_start: 0.8885 (t0) cc_final: 0.8662 (t0) REVERT: M 307 TRP cc_start: 0.9044 (m100) cc_final: 0.8500 (m100) REVERT: N 97 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9070 (tpt) REVERT: N 117 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8140 (mm-30) REVERT: N 139 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9158 (mt) REVERT: N 146 TYR cc_start: 0.9456 (p90) cc_final: 0.9248 (p90) REVERT: O 265 ASP cc_start: 0.8831 (t70) cc_final: 0.8484 (t0) REVERT: U 29 LYS cc_start: 0.9474 (mmmm) cc_final: 0.9233 (ttmm) REVERT: U 37 MET cc_start: 0.9265 (mpt) cc_final: 0.8671 (mpt) REVERT: U 49 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8776 (mt-10) REVERT: X 89 ASP cc_start: 0.9541 (t70) cc_final: 0.9220 (t0) REVERT: Y 1 VAL cc_start: 0.8652 (m) cc_final: 0.8280 (p) REVERT: Y 2 LYS cc_start: 0.8993 (mppt) cc_final: 0.8726 (mmtp) REVERT: b 14 LYS cc_start: 0.9403 (ptpt) cc_final: 0.9142 (ptpp) REVERT: c 6 GLU cc_start: 0.9019 (tp30) cc_final: 0.8729 (tp30) REVERT: c 37 GLU cc_start: 0.9399 (tp30) cc_final: 0.8799 (tm-30) REVERT: d 9 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8965 (mm-30) REVERT: d 25 LYS cc_start: 0.8901 (ttpm) cc_final: 0.8606 (ptmm) REVERT: e 18 MET cc_start: 0.9291 (tpp) cc_final: 0.9040 (mmt) REVERT: h 6 LYS cc_start: 0.8084 (tppp) cc_final: 0.7141 (mmtt) REVERT: i 12 GLN cc_start: 0.9209 (mt0) cc_final: 0.8904 (mt0) REVERT: i 16 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8818 (tp30) REVERT: i 23 LYS cc_start: 0.9627 (tptm) cc_final: 0.9366 (tppp) REVERT: i 92 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9066 (mppt) REVERT: i 121 ASP cc_start: 0.8688 (m-30) cc_final: 0.8323 (p0) REVERT: j 13 GLU cc_start: 0.9582 (OUTLIER) cc_final: 0.9355 (mp0) REVERT: j 55 ASP cc_start: 0.8997 (t70) cc_final: 0.8541 (t0) REVERT: j 58 GLN cc_start: 0.9378 (mm110) cc_final: 0.9082 (mm-40) REVERT: k 20 GLU cc_start: 0.9283 (tp30) cc_final: 0.9057 (tp30) REVERT: m 61 ASP cc_start: 0.9244 (t70) cc_final: 0.9001 (t0) REVERT: m 107 ASP cc_start: 0.9485 (t0) cc_final: 0.9148 (t0) REVERT: n 52 ASN cc_start: 0.8919 (m-40) cc_final: 0.8535 (m-40) REVERT: n 113 MET cc_start: 0.9532 (mtp) cc_final: 0.9307 (ttm) REVERT: p 37 ASP cc_start: 0.9103 (m-30) cc_final: 0.8821 (m-30) REVERT: p 80 ASP cc_start: 0.9015 (t0) cc_final: 0.8687 (t0) outliers start: 135 outliers final: 78 residues processed: 1077 average time/residue: 1.4948 time to fit residues: 2111.5071 Evaluate side-chains 1061 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 976 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 44 ASP Chi-restraints excluded: chain 6 residue 59 THR Chi-restraints excluded: chain 6 residue 60 PHE Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 617 ASP Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain W residue 67 GLU Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain r residue 39 LYS Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain X residue 93 MET Chi-restraints excluded: chain X residue 133 ASP Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Y residue 106 SER Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 117 GLU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 58 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 2.9990 chunk 305 optimal weight: 7.9990 chunk 456 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 485 optimal weight: 4.9990 chunk 520 optimal weight: 8.9990 chunk 377 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 600 optimal weight: 0.0980 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN P 250 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN W 101 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN J 2 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 572 ASN ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 3 ASN d 8 HIS ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 ASN m 49 GLN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.268 68775 Z= 0.543 Angle : 1.579 50.872 93017 Z= 1.018 Chirality : 0.310 6.492 10122 Planarity : 0.004 0.060 11606 Dihedral : 9.895 174.185 10190 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 1.79 % Allowed : 16.60 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.10), residues: 8031 helix: 1.73 (0.08), residues: 4399 sheet: -0.05 (0.25), residues: 432 loop : 0.01 (0.12), residues: 3200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP P 326 HIS 0.006 0.001 HIS 9 67 PHE 0.034 0.001 PHE l 1 TYR 0.035 0.001 TYR N 146 ARG 0.015 0.000 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1014 time to evaluate : 6.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 44 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8752 (m-30) REVERT: 6 112 LYS cc_start: 0.9338 (ttmm) cc_final: 0.9115 (ttpp) REVERT: 6 119 GLU cc_start: 0.8648 (tp30) cc_final: 0.8250 (tp30) REVERT: D 164 MET cc_start: 0.8790 (ptp) cc_final: 0.8590 (ptt) REVERT: 9 14 VAL cc_start: 0.8773 (t) cc_final: 0.8570 (p) REVERT: Q 16 LYS cc_start: 0.9054 (mppt) cc_final: 0.8688 (ttpp) REVERT: Q 28 GLU cc_start: 0.9174 (tt0) cc_final: 0.8901 (tm-30) REVERT: 7 51 GLU cc_start: 0.8852 (tp30) cc_final: 0.8446 (tp30) REVERT: T 35 HIS cc_start: 0.8708 (t-90) cc_final: 0.8299 (t-90) REVERT: T 47 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8926 (tm-30) REVERT: T 52 MET cc_start: 0.8867 (mtm) cc_final: 0.8609 (ttm) REVERT: V 63 ASP cc_start: 0.9190 (t0) cc_final: 0.8906 (t0) REVERT: W 59 LYS cc_start: 0.9245 (tptp) cc_final: 0.8724 (tmtm) REVERT: W 63 ASP cc_start: 0.8970 (m-30) cc_final: 0.8444 (m-30) REVERT: H 59 GLU cc_start: 0.8232 (pp20) cc_final: 0.7976 (pp20) REVERT: J 63 MET cc_start: 0.9407 (tpt) cc_final: 0.9186 (tpp) REVERT: J 69 TYR cc_start: 0.9291 (t80) cc_final: 0.9085 (t80) REVERT: J 91 PHE cc_start: 0.8116 (m-80) cc_final: 0.7836 (m-80) REVERT: J 122 ASP cc_start: 0.9406 (m-30) cc_final: 0.8967 (m-30) REVERT: J 125 MET cc_start: 0.9330 (mmm) cc_final: 0.9058 (mmm) REVERT: K 88 ASP cc_start: 0.9356 (p0) cc_final: 0.9081 (p0) REVERT: L 145 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.8683 (mp0) REVERT: L 267 THR cc_start: 0.9469 (m) cc_final: 0.9227 (p) REVERT: L 476 SER cc_start: 0.8472 (m) cc_final: 0.8134 (t) REVERT: L 539 MET cc_start: 0.9491 (tmm) cc_final: 0.9158 (tmm) REVERT: L 559 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8796 (tp30) REVERT: M 87 ASP cc_start: 0.8700 (t0) cc_final: 0.8279 (t70) REVERT: M 114 GLU cc_start: 0.9019 (tp30) cc_final: 0.8677 (tp30) REVERT: M 123 GLU cc_start: 0.9222 (mp0) cc_final: 0.8824 (mp0) REVERT: M 307 TRP cc_start: 0.9018 (m100) cc_final: 0.8454 (m100) REVERT: M 310 MET cc_start: 0.9336 (tmm) cc_final: 0.8024 (ttm) REVERT: M 383 MET cc_start: 0.8866 (ptm) cc_final: 0.8625 (ptt) REVERT: N 97 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.9068 (tpt) REVERT: N 117 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8141 (mm-30) REVERT: N 139 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9154 (mt) REVERT: O 30 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8583 (t0) REVERT: O 265 ASP cc_start: 0.8842 (t70) cc_final: 0.8504 (t0) REVERT: U 29 LYS cc_start: 0.9465 (mmmm) cc_final: 0.9226 (ttmm) REVERT: U 37 MET cc_start: 0.9245 (mpt) cc_final: 0.8675 (mpt) REVERT: X 89 ASP cc_start: 0.9537 (t70) cc_final: 0.9231 (t0) REVERT: b 14 LYS cc_start: 0.9390 (ptpt) cc_final: 0.9134 (ptpp) REVERT: c 6 GLU cc_start: 0.9033 (tp30) cc_final: 0.8741 (tp30) REVERT: c 37 GLU cc_start: 0.9405 (tp30) cc_final: 0.9188 (tp30) REVERT: d 9 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8961 (mm-30) REVERT: d 25 LYS cc_start: 0.8894 (ttpm) cc_final: 0.8592 (ptmm) REVERT: e 18 MET cc_start: 0.9283 (tpp) cc_final: 0.9060 (mmt) REVERT: g 22 MET cc_start: 0.0941 (mmp) cc_final: 0.0152 (mmm) REVERT: g 46 ASP cc_start: 0.9100 (t70) cc_final: 0.8497 (t70) REVERT: i 12 GLN cc_start: 0.9206 (mt0) cc_final: 0.8900 (mt0) REVERT: i 16 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8819 (tp30) REVERT: i 23 LYS cc_start: 0.9627 (tptm) cc_final: 0.9368 (tppp) REVERT: i 92 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9060 (mppt) REVERT: j 13 GLU cc_start: 0.9578 (OUTLIER) cc_final: 0.9360 (mp0) REVERT: j 55 ASP cc_start: 0.8995 (t70) cc_final: 0.8630 (t0) REVERT: j 58 GLN cc_start: 0.9376 (mm110) cc_final: 0.9122 (mm-40) REVERT: l 148 GLU cc_start: 0.9261 (tp30) cc_final: 0.9052 (tp30) REVERT: m 27 GLU cc_start: 0.9364 (pm20) cc_final: 0.9070 (pm20) REVERT: m 61 ASP cc_start: 0.9264 (t70) cc_final: 0.9014 (t0) REVERT: m 107 ASP cc_start: 0.9465 (t0) cc_final: 0.9123 (t0) REVERT: m 112 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8792 (mm-30) REVERT: m 116 GLN cc_start: 0.9408 (mm110) cc_final: 0.9020 (mm110) REVERT: m 117 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8973 (pm20) REVERT: n 52 ASN cc_start: 0.8923 (m-40) cc_final: 0.8548 (m-40) REVERT: n 113 MET cc_start: 0.9521 (mtp) cc_final: 0.9305 (ttm) REVERT: n 122 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.9032 (mm-30) REVERT: o 17 ASP cc_start: 0.8371 (p0) cc_final: 0.8045 (p0) REVERT: p 37 ASP cc_start: 0.9085 (m-30) cc_final: 0.8809 (m-30) REVERT: p 80 ASP cc_start: 0.9015 (t0) cc_final: 0.8723 (t0) outliers start: 128 outliers final: 75 residues processed: 1076 average time/residue: 1.5406 time to fit residues: 2166.8829 Evaluate side-chains 1063 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 979 time to evaluate : 5.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 44 ASP Chi-restraints excluded: chain 6 residue 59 THR Chi-restraints excluded: chain 6 residue 60 PHE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 617 ASP Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 326 TRP Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain W residue 67 GLU Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain O residue 30 ASN Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain X residue 93 MET Chi-restraints excluded: chain X residue 133 ASP Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Z residue 19 ASP Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 117 GLU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 58 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 695 optimal weight: 2.9990 chunk 732 optimal weight: 6.9990 chunk 668 optimal weight: 20.0000 chunk 712 optimal weight: 0.9990 chunk 428 optimal weight: 20.0000 chunk 310 optimal weight: 2.9990 chunk 559 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 643 optimal weight: 0.0000 chunk 673 optimal weight: 6.9990 chunk 709 optimal weight: 3.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 172 GLN P 250 HIS Q 43 ASN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN J 2 ASN J 107 ASN ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 3 ASN ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 42 GLN o 53 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.266 68775 Z= 0.531 Angle : 1.578 50.815 93017 Z= 1.017 Chirality : 0.310 6.471 10122 Planarity : 0.004 0.059 11606 Dihedral : 9.740 174.829 10190 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.37 % Favored : 96.61 % Rotamer: Outliers : 1.58 % Allowed : 16.98 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.10), residues: 8031 helix: 1.73 (0.08), residues: 4397 sheet: 0.03 (0.25), residues: 427 loop : 0.03 (0.12), residues: 3207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP P 326 HIS 0.006 0.001 HIS L 332 PHE 0.024 0.001 PHE M 151 TYR 0.044 0.001 TYR N 146 ARG 0.013 0.000 ARG m 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1019 time to evaluate : 6.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 44 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8734 (m-30) REVERT: 6 112 LYS cc_start: 0.9321 (ttmm) cc_final: 0.9093 (ttpp) REVERT: 6 119 GLU cc_start: 0.8610 (tp30) cc_final: 0.8270 (tp30) REVERT: 9 14 VAL cc_start: 0.8750 (t) cc_final: 0.8542 (p) REVERT: Q 16 LYS cc_start: 0.9045 (mppt) cc_final: 0.8557 (ttpp) REVERT: Q 28 GLU cc_start: 0.9160 (tt0) cc_final: 0.8891 (tm-30) REVERT: 7 51 GLU cc_start: 0.8841 (tp30) cc_final: 0.8437 (tp30) REVERT: T 47 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8949 (tm-30) REVERT: T 52 MET cc_start: 0.8846 (mtm) cc_final: 0.8571 (ttm) REVERT: V 63 ASP cc_start: 0.9192 (t0) cc_final: 0.8914 (t0) REVERT: W 59 LYS cc_start: 0.9255 (tptp) cc_final: 0.8721 (tmtm) REVERT: W 63 ASP cc_start: 0.8966 (m-30) cc_final: 0.8429 (m-30) REVERT: r 107 LYS cc_start: 0.9667 (mtmm) cc_final: 0.9405 (mmpt) REVERT: H 59 GLU cc_start: 0.8180 (pp20) cc_final: 0.7914 (pp20) REVERT: H 258 ASN cc_start: 0.9286 (OUTLIER) cc_final: 0.8579 (t0) REVERT: J 63 MET cc_start: 0.9385 (tpt) cc_final: 0.9115 (tpp) REVERT: J 91 PHE cc_start: 0.8090 (m-80) cc_final: 0.7797 (m-80) REVERT: J 122 ASP cc_start: 0.9390 (m-30) cc_final: 0.8960 (m-30) REVERT: J 125 MET cc_start: 0.9340 (mmm) cc_final: 0.9074 (mmm) REVERT: K 10 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.9153 (mmm) REVERT: K 88 ASP cc_start: 0.9270 (p0) cc_final: 0.9000 (p0) REVERT: L 145 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8661 (mp0) REVERT: L 237 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7886 (mmt) REVERT: L 267 THR cc_start: 0.9464 (m) cc_final: 0.9225 (p) REVERT: L 476 SER cc_start: 0.8413 (m) cc_final: 0.8068 (t) REVERT: L 539 MET cc_start: 0.9492 (tmm) cc_final: 0.9154 (tmm) REVERT: M 87 ASP cc_start: 0.8715 (t0) cc_final: 0.8330 (t70) REVERT: M 114 GLU cc_start: 0.9012 (tp30) cc_final: 0.8643 (tp30) REVERT: M 123 GLU cc_start: 0.9203 (mp0) cc_final: 0.8800 (mp0) REVERT: M 307 TRP cc_start: 0.8980 (m100) cc_final: 0.8459 (m100) REVERT: N 97 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.9062 (tpt) REVERT: N 117 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8163 (mm-30) REVERT: O 265 ASP cc_start: 0.8842 (t70) cc_final: 0.8518 (t0) REVERT: U 26 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8629 (p0) REVERT: U 28 GLU cc_start: 0.9160 (pm20) cc_final: 0.8870 (pm20) REVERT: U 29 LYS cc_start: 0.9467 (mmmm) cc_final: 0.9106 (ttmm) REVERT: U 37 MET cc_start: 0.9238 (mpt) cc_final: 0.8745 (mpt) REVERT: X 89 ASP cc_start: 0.9527 (t70) cc_final: 0.9219 (t0) REVERT: c 6 GLU cc_start: 0.8988 (tp30) cc_final: 0.8688 (tp30) REVERT: c 37 GLU cc_start: 0.9411 (tp30) cc_final: 0.9197 (tp30) REVERT: d 9 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8961 (mm-30) REVERT: d 25 LYS cc_start: 0.8836 (ttpm) cc_final: 0.8545 (ptmm) REVERT: e 18 MET cc_start: 0.9260 (tpp) cc_final: 0.9007 (mmt) REVERT: g 22 MET cc_start: 0.0759 (mmp) cc_final: -0.0006 (mmm) REVERT: g 46 ASP cc_start: 0.9067 (t70) cc_final: 0.8442 (t70) REVERT: h 6 LYS cc_start: 0.8031 (tppp) cc_final: 0.7051 (mmtt) REVERT: i 12 GLN cc_start: 0.9200 (mt0) cc_final: 0.8895 (mt0) REVERT: i 16 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8838 (tp30) REVERT: i 23 LYS cc_start: 0.9606 (tptm) cc_final: 0.9346 (tppp) REVERT: i 92 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9032 (mppt) REVERT: j 13 GLU cc_start: 0.9577 (OUTLIER) cc_final: 0.9340 (mp0) REVERT: j 55 ASP cc_start: 0.9024 (t70) cc_final: 0.8659 (t0) REVERT: j 58 GLN cc_start: 0.9370 (mm110) cc_final: 0.9125 (mm-40) REVERT: l 148 GLU cc_start: 0.9268 (tp30) cc_final: 0.8951 (tp30) REVERT: m 27 GLU cc_start: 0.9364 (pm20) cc_final: 0.9072 (pm20) REVERT: m 61 ASP cc_start: 0.9253 (t70) cc_final: 0.9005 (t0) REVERT: m 107 ASP cc_start: 0.9410 (t0) cc_final: 0.9095 (t0) REVERT: m 112 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8362 (mm-30) REVERT: m 116 GLN cc_start: 0.9410 (mm110) cc_final: 0.8895 (mp10) REVERT: m 117 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8959 (pm20) REVERT: n 52 ASN cc_start: 0.8906 (m-40) cc_final: 0.8540 (m-40) REVERT: n 72 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8719 (mm110) REVERT: n 113 MET cc_start: 0.9502 (mtp) cc_final: 0.9296 (ttm) REVERT: n 122 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.9025 (mm-30) REVERT: o 17 ASP cc_start: 0.8558 (p0) cc_final: 0.8039 (p0) REVERT: o 19 GLU cc_start: 0.8968 (mp0) cc_final: 0.8706 (pm20) REVERT: p 37 ASP cc_start: 0.9078 (m-30) cc_final: 0.8804 (m-30) REVERT: p 80 ASP cc_start: 0.9018 (t0) cc_final: 0.8746 (t0) outliers start: 113 outliers final: 60 residues processed: 1077 average time/residue: 1.5178 time to fit residues: 2137.0728 Evaluate side-chains 1059 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 988 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 44 ASP Chi-restraints excluded: chain 6 residue 59 THR Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 609 ILE Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain 9 residue 128 CYS Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 326 TRP Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain T residue 33 ASN Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain W residue 67 GLU Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 237 MET Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain X residue 93 MET Chi-restraints excluded: chain X residue 133 ASP Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 19 ASP Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 10 ASN Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 117 GLU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain o residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 10.0000 chunk 753 optimal weight: 5.9990 chunk 459 optimal weight: 9.9990 chunk 357 optimal weight: 0.0570 chunk 523 optimal weight: 20.0000 chunk 790 optimal weight: 7.9990 chunk 727 optimal weight: 4.9990 chunk 629 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 485 optimal weight: 3.9990 chunk 385 optimal weight: 20.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 250 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN W 101 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 125 HIS ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.264 68775 Z= 0.553 Angle : 1.604 59.200 93017 Z= 1.031 Chirality : 0.310 6.478 10122 Planarity : 0.004 0.076 11606 Dihedral : 9.736 174.802 10190 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.39 % Favored : 96.60 % Rotamer: Outliers : 1.33 % Allowed : 17.61 % Favored : 81.06 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.10), residues: 8031 helix: 1.72 (0.08), residues: 4391 sheet: 0.03 (0.25), residues: 427 loop : 0.02 (0.12), residues: 3213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP P 326 HIS 0.005 0.001 HIS 9 67 PHE 0.025 0.001 PHE M 151 TYR 0.043 0.001 TYR N 146 ARG 0.017 0.000 ARG S 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 986 time to evaluate : 5.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 44 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8735 (m-30) REVERT: 6 112 LYS cc_start: 0.9322 (ttmm) cc_final: 0.9095 (ttpp) REVERT: 6 119 GLU cc_start: 0.8612 (tp30) cc_final: 0.8270 (tp30) REVERT: 9 14 VAL cc_start: 0.8751 (t) cc_final: 0.8538 (p) REVERT: Q 16 LYS cc_start: 0.9052 (mppt) cc_final: 0.8557 (ttpp) REVERT: Q 28 GLU cc_start: 0.9154 (tt0) cc_final: 0.8900 (tm-30) REVERT: 7 51 GLU cc_start: 0.8842 (tp30) cc_final: 0.8438 (tp30) REVERT: T 35 HIS cc_start: 0.8304 (t-90) cc_final: 0.7811 (t-90) REVERT: T 47 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8949 (tm-30) REVERT: V 63 ASP cc_start: 0.9193 (t0) cc_final: 0.8915 (t0) REVERT: W 59 LYS cc_start: 0.9255 (tptp) cc_final: 0.8724 (tmtm) REVERT: W 63 ASP cc_start: 0.8967 (m-30) cc_final: 0.8431 (m-30) REVERT: r 107 LYS cc_start: 0.9667 (mtmm) cc_final: 0.9407 (mmpt) REVERT: H 59 GLU cc_start: 0.8181 (pp20) cc_final: 0.7913 (pp20) REVERT: J 63 MET cc_start: 0.9379 (tpt) cc_final: 0.9112 (tpp) REVERT: J 91 PHE cc_start: 0.8090 (m-80) cc_final: 0.7797 (m-80) REVERT: J 108 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: J 122 ASP cc_start: 0.9383 (m-30) cc_final: 0.8945 (m-30) REVERT: J 125 MET cc_start: 0.9336 (mmm) cc_final: 0.9074 (mmm) REVERT: K 10 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.9153 (mmm) REVERT: K 88 ASP cc_start: 0.9269 (p0) cc_final: 0.9000 (p0) REVERT: L 71 MET cc_start: 0.8813 (mtp) cc_final: 0.8303 (mtp) REVERT: L 145 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8663 (mp0) REVERT: L 237 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7887 (mmt) REVERT: L 267 THR cc_start: 0.9466 (m) cc_final: 0.9225 (p) REVERT: L 476 SER cc_start: 0.8433 (m) cc_final: 0.8063 (t) REVERT: L 482 MET cc_start: 0.9580 (OUTLIER) cc_final: 0.9010 (ppp) REVERT: L 539 MET cc_start: 0.9494 (tmm) cc_final: 0.9164 (tmm) REVERT: M 87 ASP cc_start: 0.8719 (t0) cc_final: 0.8329 (t70) REVERT: M 114 GLU cc_start: 0.9011 (tp30) cc_final: 0.8640 (tp30) REVERT: M 123 GLU cc_start: 0.9204 (mp0) cc_final: 0.8809 (mp0) REVERT: M 307 TRP cc_start: 0.8969 (m100) cc_final: 0.8408 (m100) REVERT: M 310 MET cc_start: 0.9255 (tmm) cc_final: 0.7961 (ttm) REVERT: N 97 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.9062 (tpt) REVERT: N 117 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8153 (mm-30) REVERT: N 323 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8050 (p0) REVERT: O 265 ASP cc_start: 0.8845 (t70) cc_final: 0.8515 (t0) REVERT: U 26 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8627 (p0) REVERT: U 28 GLU cc_start: 0.9160 (pm20) cc_final: 0.8871 (pm20) REVERT: U 29 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9107 (ttmm) REVERT: U 37 MET cc_start: 0.9234 (mpt) cc_final: 0.8741 (mpt) REVERT: X 89 ASP cc_start: 0.9528 (t70) cc_final: 0.9222 (t0) REVERT: b 14 LYS cc_start: 0.9290 (ptpt) cc_final: 0.8910 (mptp) REVERT: c 6 GLU cc_start: 0.8999 (tp30) cc_final: 0.8698 (tp30) REVERT: c 37 GLU cc_start: 0.9412 (tp30) cc_final: 0.9196 (tp30) REVERT: d 9 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8961 (mm-30) REVERT: d 25 LYS cc_start: 0.8837 (ttpm) cc_final: 0.8543 (ptmm) REVERT: e 18 MET cc_start: 0.9263 (tpp) cc_final: 0.9010 (mmt) REVERT: g 22 MET cc_start: 0.0759 (mmp) cc_final: -0.0003 (mmm) REVERT: g 46 ASP cc_start: 0.9071 (t70) cc_final: 0.8447 (t70) REVERT: h 6 LYS cc_start: 0.8031 (tppp) cc_final: 0.7052 (mmtt) REVERT: i 12 GLN cc_start: 0.9200 (mt0) cc_final: 0.8895 (mt0) REVERT: i 16 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8838 (tp30) REVERT: i 23 LYS cc_start: 0.9606 (tptm) cc_final: 0.9346 (tppp) REVERT: i 92 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9033 (mppt) REVERT: j 13 GLU cc_start: 0.9578 (OUTLIER) cc_final: 0.9340 (mp0) REVERT: j 55 ASP cc_start: 0.9024 (t70) cc_final: 0.8659 (t0) REVERT: j 58 GLN cc_start: 0.9370 (mm110) cc_final: 0.9125 (mm-40) REVERT: l 148 GLU cc_start: 0.9271 (tp30) cc_final: 0.8923 (tp30) REVERT: m 27 GLU cc_start: 0.9364 (pm20) cc_final: 0.9075 (pm20) REVERT: m 61 ASP cc_start: 0.9253 (t70) cc_final: 0.9005 (t0) REVERT: m 107 ASP cc_start: 0.9411 (t0) cc_final: 0.9096 (t0) REVERT: m 112 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8355 (mm-30) REVERT: m 116 GLN cc_start: 0.9411 (mm110) cc_final: 0.8892 (mp10) REVERT: m 117 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8958 (pm20) REVERT: n 52 ASN cc_start: 0.8911 (m-40) cc_final: 0.8534 (m-40) REVERT: n 72 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8721 (mm110) REVERT: n 113 MET cc_start: 0.9503 (mtp) cc_final: 0.9297 (ttm) REVERT: n 122 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.9028 (mm-30) REVERT: o 19 GLU cc_start: 0.8985 (mp0) cc_final: 0.8703 (pm20) REVERT: p 37 ASP cc_start: 0.9078 (m-30) cc_final: 0.8804 (m-30) REVERT: p 80 ASP cc_start: 0.9019 (t0) cc_final: 0.8746 (t0) outliers start: 95 outliers final: 64 residues processed: 1032 average time/residue: 1.5109 time to fit residues: 2035.4153 Evaluate side-chains 1063 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 986 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 44 ASP Chi-restraints excluded: chain 6 residue 59 THR Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 3 residue 19 MET Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 609 ILE Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 326 TRP Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 33 ASN Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain W residue 67 GLU Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 237 MET Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 383 MET Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 323 ASN Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain X residue 93 MET Chi-restraints excluded: chain X residue 133 ASP Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 19 ASP Chi-restraints excluded: chain Z residue 71 MET Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 117 GLU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 0.0980 chunk 670 optimal weight: 7.9990 chunk 192 optimal weight: 0.3980 chunk 580 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 630 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 647 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 250 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN W 101 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN J 107 ASN ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 3 ASN ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.043070 restraints weight = 209282.422| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.44 r_work: 0.2569 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.264 68775 Z= 0.553 Angle : 1.604 59.200 93017 Z= 1.031 Chirality : 0.310 6.478 10122 Planarity : 0.004 0.076 11606 Dihedral : 9.736 174.802 10190 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.39 % Favored : 96.60 % Rotamer: Outliers : 1.12 % Allowed : 17.85 % Favored : 81.03 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.10), residues: 8031 helix: 1.72 (0.08), residues: 4391 sheet: 0.03 (0.25), residues: 427 loop : 0.02 (0.12), residues: 3213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP P 326 HIS 0.005 0.001 HIS 9 67 PHE 0.025 0.001 PHE M 151 TYR 0.043 0.001 TYR N 146 ARG 0.017 0.000 ARG S 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28049.37 seconds wall clock time: 484 minutes 54.74 seconds (29094.74 seconds total)