Starting phenix.real_space_refine on Fri Apr 12 22:38:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/04_2024/8y7e_39013_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/04_2024/8y7e_39013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/04_2024/8y7e_39013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/04_2024/8y7e_39013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/04_2024/8y7e_39013_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/04_2024/8y7e_39013_updated.pdb" } resolution = 4.66 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 82 5.49 5 S 126 5.16 5 C 16673 2.51 5 N 4747 2.21 5 O 5317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 108": "NH1" <-> "NH2" Residue "1 ARG 115": "NH1" <-> "NH2" Residue "1 ARG 123": "NH1" <-> "NH2" Residue "1 ARG 124": "NH1" <-> "NH2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 ARG 157": "NH1" <-> "NH2" Residue "1 ARG 166": "NH1" <-> "NH2" Residue "1 ARG 169": "NH1" <-> "NH2" Residue "1 ARG 451": "NH1" <-> "NH2" Residue "1 ARG 495": "NH1" <-> "NH2" Residue "1 ARG 517": "NH1" <-> "NH2" Residue "1 ARG 590": "NH1" <-> "NH2" Residue "1 ARG 614": "NH1" <-> "NH2" Residue "1 ARG 684": "NH1" <-> "NH2" Residue "1 GLU 691": "OE1" <-> "OE2" Residue "1 ARG 736": "NH1" <-> "NH2" Residue "1 ARG 767": "NH1" <-> "NH2" Residue "1 ARG 822": "NH1" <-> "NH2" Residue "1 GLU 870": "OE1" <-> "OE2" Residue "1 ARG 939": "NH1" <-> "NH2" Residue "1 ARG 1019": "NH1" <-> "NH2" Residue "1 ARG 1027": "NH1" <-> "NH2" Residue "1 ARG 1045": "NH1" <-> "NH2" Residue "1 ARG 1053": "NH1" <-> "NH2" Residue "1 ARG 1106": "NH1" <-> "NH2" Residue "1 PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 1180": "NH1" <-> "NH2" Residue "1 ARG 1245": "NH1" <-> "NH2" Residue "2 ARG 515": "NH1" <-> "NH2" Residue "2 PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 530": "NH1" <-> "NH2" Residue "2 ARG 554": "NH1" <-> "NH2" Residue "3 GLU 136": "OE1" <-> "OE2" Residue "3 GLU 186": "OE1" <-> "OE2" Residue "3 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 274": "NH1" <-> "NH2" Residue "3 ARG 275": "NH1" <-> "NH2" Residue "3 PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 326": "NH1" <-> "NH2" Residue "3 ARG 429": "NH1" <-> "NH2" Residue "3 ARG 464": "NH1" <-> "NH2" Residue "3 GLU 469": "OE1" <-> "OE2" Residue "3 GLU 492": "OE1" <-> "OE2" Residue "3 ARG 528": "NH1" <-> "NH2" Residue "3 GLU 644": "OE1" <-> "OE2" Residue "3 ARG 718": "NH1" <-> "NH2" Residue "3 GLU 740": "OE1" <-> "OE2" Residue "3 PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 815": "NH1" <-> "NH2" Residue "3 ARG 895": "NH1" <-> "NH2" Residue "3 TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 982": "OE1" <-> "OE2" Residue "3 ARG 999": "NH1" <-> "NH2" Residue "3 GLU 1007": "OE1" <-> "OE2" Residue "3 ARG 1013": "NH1" <-> "NH2" Residue "3 ARG 1079": "NH1" <-> "NH2" Residue "5 ARG 19": "NH1" <-> "NH2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "5 ARG 85": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 57": "NH1" <-> "NH2" Residue "6 ARG 102": "NH1" <-> "NH2" Residue "v ARG 5": "NH1" <-> "NH2" Residue "v ARG 19": "NH1" <-> "NH2" Residue "v ARG 20": "NH1" <-> "NH2" Residue "v ARG 38": "NH1" <-> "NH2" Residue "v ARG 41": "NH1" <-> "NH2" Residue "v ARG 50": "NH1" <-> "NH2" Residue "v ARG 63": "NH1" <-> "NH2" Residue "v ARG 187": "NH1" <-> "NH2" Residue "v GLU 223": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26949 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 5, 'rna3p_pyr': 18} Link IDs: {'rna2p': 7, 'rna3p': 22} Chain: "1" Number of atoms: 7766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7766 Classifications: {'peptide': 971} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 919} Chain breaks: 2 Chain: "2" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1674 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 194} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "3" Number of atoms: 9352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1193, 9352 Classifications: {'peptide': 1193} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1132} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 383 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 135 Chain: "5" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 906 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "6" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "7" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 669 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1079 Classifications: {'RNA': 50} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 29, 'rna3p_pyr': 14} Link IDs: {'rna2p': 7, 'rna3p': 42} Chain breaks: 1 Chain: "h" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 393 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "i" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 422 Classifications: {'peptide': 86} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "j" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "k" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 422 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "l" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "m" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 361 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "n" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 334 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "v" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 963 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20863 SG CYS 6 23 71.908 95.780 137.370 1.00 22.26 S ATOM 20887 SG CYS 6 26 72.384 93.618 134.617 1.00 23.62 S ATOM 21134 SG CYS 6 58 74.130 92.569 137.592 1.00 22.59 S ATOM 21155 SG CYS 6 61 75.284 95.786 136.138 1.00 28.41 S ATOM 20776 SG CYS 6 11 85.713 83.466 138.007 1.00 13.91 S ATOM 21039 SG CYS 6 46 84.877 82.601 141.601 1.00 22.59 S ATOM 21062 SG CYS 6 49 84.275 85.965 140.376 1.00 27.92 S ATOM 21333 SG CYS 6 85 82.158 83.128 139.062 1.00 15.57 S ATOM 20914 SG CYS 6 30 70.390 82.475 130.699 1.00 15.44 S ATOM 20935 SG CYS 6 33 69.815 82.625 127.055 1.00 35.11 S ATOM 21230 SG CYS 6 72 67.891 80.201 128.908 1.00 17.24 S ATOM 21254 SG CYS 6 75 71.484 79.574 128.439 1.00 35.11 S ATOM 26340 SG CYS v 44 71.844 96.791 84.562 1.00 26.97 S ATOM 26359 SG CYS v 47 75.532 96.340 83.803 1.00 37.41 S Time building chain proxies: 14.61, per 1000 atoms: 0.54 Number of scatterers: 26949 At special positions: 0 Unit cell: (166.501, 164.353, 191.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 126 16.00 P 82 15.00 O 5317 8.00 N 4747 7.00 C 16673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 11.60 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 6 201 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 61 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 23 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 26 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 58 " pdb=" ZN 6 202 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 49 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 46 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 85 " pdb=" ZN 6 203 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 33 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 72 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 30 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 75 " pdb=" ZN v 300 " pdb="ZN ZN v 300 " - pdb=" ND1 HIS v 68 " pdb="ZN ZN v 300 " - pdb=" SG CYS v 44 " pdb="ZN ZN v 300 " - pdb=" NE2 HIS v 62 " pdb="ZN ZN v 300 " - pdb=" SG CYS v 47 " Number of angles added : 20 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6406 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 41 sheets defined 33.7% alpha, 20.6% beta 16 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 13.67 Creating SS restraints... Processing helix chain '1' and resid 103 through 106 removed outlier: 4.386A pdb=" N GLU 1 106 " --> pdb=" O PRO 1 103 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 103 through 106' Processing helix chain '1' and resid 120 through 124 Processing helix chain '1' and resid 137 through 140 No H-bonds generated for 'chain '1' and resid 137 through 140' Processing helix chain '1' and resid 152 through 175 removed outlier: 3.791A pdb=" N GLU 1 174 " --> pdb=" O GLN 1 170 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS 1 175 " --> pdb=" O GLN 1 171 " (cutoff:3.500A) Processing helix chain '1' and resid 401 through 407 removed outlier: 3.792A pdb=" N ASP 1 405 " --> pdb=" O ASP 1 401 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA 1 406 " --> pdb=" O GLU 1 402 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET 1 407 " --> pdb=" O GLU 1 403 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 401 through 407' Processing helix chain '1' and resid 452 through 455 No H-bonds generated for 'chain '1' and resid 452 through 455' Processing helix chain '1' and resid 469 through 471 No H-bonds generated for 'chain '1' and resid 469 through 471' Processing helix chain '1' and resid 476 through 478 No H-bonds generated for 'chain '1' and resid 476 through 478' Processing helix chain '1' and resid 489 through 506 Processing helix chain '1' and resid 509 through 521 Processing helix chain '1' and resid 523 through 526 No H-bonds generated for 'chain '1' and resid 523 through 526' Processing helix chain '1' and resid 528 through 539 removed outlier: 3.986A pdb=" N GLN 1 534 " --> pdb=" O PRO 1 530 " (cutoff:3.500A) Proline residue: 1 537 - end of helix Processing helix chain '1' and resid 546 through 562 removed outlier: 3.913A pdb=" N TYR 1 561 " --> pdb=" O ASP 1 557 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS 1 562 " --> pdb=" O ARG 1 558 " (cutoff:3.500A) Processing helix chain '1' and resid 568 through 583 removed outlier: 5.103A pdb=" N HIS 1 572 " --> pdb=" O PRO 1 569 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS 1 573 " --> pdb=" O TYR 1 570 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL 1 576 " --> pdb=" O LYS 1 573 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLU 1 579 " --> pdb=" O VAL 1 576 " (cutoff:3.500A) Proline residue: 1 580 - end of helix Processing helix chain '1' and resid 587 through 604 Processing helix chain '1' and resid 606 through 617 Proline residue: 1 615 - end of helix Processing helix chain '1' and resid 622 through 639 removed outlier: 3.808A pdb=" N ALA 1 633 " --> pdb=" O ALA 1 629 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL 1 634 " --> pdb=" O ARG 1 630 " (cutoff:3.500A) Processing helix chain '1' and resid 641 through 652 Proline residue: 1 646 - end of helix Processing helix chain '1' and resid 658 through 693 removed outlier: 7.294A pdb=" N CYS 1 677 " --> pdb=" O ILE 1 673 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA 1 678 " --> pdb=" O LEU 1 674 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE 1 679 " --> pdb=" O MET 1 675 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU 1 680 " --> pdb=" O GLY 1 676 " (cutoff:3.500A) Proline residue: 1 681 - end of helix removed outlier: 5.065A pdb=" N ARG 1 684 " --> pdb=" O LEU 1 680 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N SER 1 685 " --> pdb=" O PRO 1 681 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU 1 688 " --> pdb=" O ARG 1 684 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE 1 689 " --> pdb=" O SER 1 685 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS 1 692 " --> pdb=" O GLU 1 688 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLY 1 693 " --> pdb=" O ILE 1 689 " (cutoff:3.500A) Processing helix chain '1' and resid 699 through 715 Processing helix chain '1' and resid 728 through 737 Processing helix chain '1' and resid 742 through 755 Proline residue: 1 755 - end of helix Processing helix chain '1' and resid 759 through 777 removed outlier: 3.660A pdb=" N TYR 1 764 " --> pdb=" O GLU 1 760 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG 1 767 " --> pdb=" O ASN 1 763 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU 1 768 " --> pdb=" O TYR 1 764 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG 1 775 " --> pdb=" O LEU 1 771 " (cutoff:3.500A) Processing helix chain '1' and resid 782 through 797 removed outlier: 3.908A pdb=" N LYS 1 790 " --> pdb=" O LYS 1 786 " (cutoff:3.500A) Processing helix chain '1' and resid 803 through 809 Processing helix chain '1' and resid 811 through 817 Processing helix chain '1' and resid 827 through 844 removed outlier: 3.742A pdb=" N LYS 1 843 " --> pdb=" O GLU 1 839 " (cutoff:3.500A) Processing helix chain '1' and resid 846 through 857 removed outlier: 4.002A pdb=" N ARG 1 852 " --> pdb=" O GLU 1 848 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE 1 853 " --> pdb=" O ILE 1 849 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP 1 855 " --> pdb=" O SER 1 851 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP 1 856 " --> pdb=" O ARG 1 852 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU 1 857 " --> pdb=" O ILE 1 853 " (cutoff:3.500A) Processing helix chain '1' and resid 862 through 878 Processing helix chain '1' and resid 886 through 902 removed outlier: 3.709A pdb=" N GLU 1 890 " --> pdb=" O HIS 1 886 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN 1 891 " --> pdb=" O LYS 1 887 " (cutoff:3.500A) Processing helix chain '1' and resid 909 through 941 removed outlier: 6.283A pdb=" N LYS 1 923 " --> pdb=" O ASN 1 919 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG 1 924 " --> pdb=" O ALA 1 920 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL 1 925 " --> pdb=" O LEU 1 921 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS 1 926 " --> pdb=" O GLY 1 922 " (cutoff:3.500A) Proline residue: 1 927 - end of helix Proline residue: 1 930 - end of helix removed outlier: 4.595A pdb=" N ASN 1 941 " --> pdb=" O LEU 1 937 " (cutoff:3.500A) Processing helix chain '1' and resid 945 through 964 removed outlier: 5.512A pdb=" N VAL 1 960 " --> pdb=" O SER 1 956 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL 1 961 " --> pdb=" O ARG 1 957 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET 1 962 " --> pdb=" O THR 1 958 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS 1 963 " --> pdb=" O ALA 1 959 " (cutoff:3.500A) Processing helix chain '1' and resid 968 through 983 removed outlier: 3.907A pdb=" N GLU 1 980 " --> pdb=" O VAL 1 976 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR 1 981 " --> pdb=" O VAL 1 977 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 1 982 " --> pdb=" O LEU 1 978 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLY 1 983 " --> pdb=" O TYR 1 979 " (cutoff:3.500A) Processing helix chain '1' and resid 987 through 1004 Processing helix chain '1' and resid 1013 through 1020 Proline residue: 11018 - end of helix Processing helix chain '1' and resid 1029 through 1045 removed outlier: 3.567A pdb=" N LEU 11038 " --> pdb=" O ASN 11034 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP 11044 " --> pdb=" O GLY 11040 " (cutoff:3.500A) Processing helix chain '1' and resid 1047 through 1049 No H-bonds generated for 'chain '1' and resid 1047 through 1049' Processing helix chain '1' and resid 1052 through 1063 removed outlier: 3.944A pdb=" N LEU 11063 " --> pdb=" O CYS 11059 " (cutoff:3.500A) Processing helix chain '1' and resid 1065 through 1067 No H-bonds generated for 'chain '1' and resid 1065 through 1067' Processing helix chain '1' and resid 1071 through 1088 removed outlier: 3.652A pdb=" N GLY 11082 " --> pdb=" O VAL 11078 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA 11087 " --> pdb=" O TYR 11083 " (cutoff:3.500A) Processing helix chain '1' and resid 1090 through 1102 removed outlier: 3.680A pdb=" N THR 11096 " --> pdb=" O ASP 11092 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU 11101 " --> pdb=" O LEU 11097 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS 11102 " --> pdb=" O LEU 11098 " (cutoff:3.500A) Processing helix chain '1' and resid 1106 through 1122 Processing helix chain '1' and resid 1125 through 1137 Proline residue: 11130 - end of helix removed outlier: 3.716A pdb=" N TYR 11136 " --> pdb=" O LEU 11132 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG 11137 " --> pdb=" O MET 11133 " (cutoff:3.500A) Processing helix chain '1' and resid 1141 through 1164 removed outlier: 7.070A pdb=" N GLU 11160 " --> pdb=" O GLU 11156 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET 11161 " --> pdb=" O TYR 11157 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY 11162 " --> pdb=" O ILE 11158 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS 11163 " --> pdb=" O GLY 11159 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASP 11164 " --> pdb=" O GLU 11160 " (cutoff:3.500A) Processing helix chain '1' and resid 1166 through 1177 Proline residue: 11171 - end of helix Processing helix chain '1' and resid 1182 through 1198 removed outlier: 3.538A pdb=" N GLY 11198 " --> pdb=" O HIS 11194 " (cutoff:3.500A) Processing helix chain '1' and resid 1205 through 1220 removed outlier: 3.820A pdb=" N TYR 11214 " --> pdb=" O HIS 11210 " (cutoff:3.500A) Proline residue: 11217 - end of helix removed outlier: 5.352A pdb=" N PHE 11220 " --> pdb=" O TRP 11216 " (cutoff:3.500A) Processing helix chain '1' and resid 1224 through 1241 removed outlier: 3.957A pdb=" N VAL 11239 " --> pdb=" O GLU 11235 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA 11240 " --> pdb=" O GLY 11236 " (cutoff:3.500A) Processing helix chain '1' and resid 1243 through 1253 removed outlier: 5.186A pdb=" N GLN 11252 " --> pdb=" O GLN 11248 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLY 11253 " --> pdb=" O TYR 11249 " (cutoff:3.500A) Processing helix chain '1' and resid 1259 through 1275 removed outlier: 3.722A pdb=" N VAL 11264 " --> pdb=" O LYS 11260 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER 11271 " --> pdb=" O LYS 11267 " (cutoff:3.500A) Processing helix chain '1' and resid 1279 through 1282 removed outlier: 3.642A pdb=" N ALA 11282 " --> pdb=" O ALA 11279 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1279 through 1282' Processing helix chain '2' and resid 462 through 468 Processing helix chain '2' and resid 479 through 481 No H-bonds generated for 'chain '2' and resid 479 through 481' Processing helix chain '2' and resid 485 through 492 Processing helix chain '2' and resid 502 through 505 removed outlier: 3.983A pdb=" N CYS 2 505 " --> pdb=" O ARG 2 502 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 502 through 505' Processing helix chain '2' and resid 514 through 518 Processing helix chain '2' and resid 526 through 531 removed outlier: 4.208A pdb=" N THR 2 531 " --> pdb=" O PHE 2 527 " (cutoff:3.500A) Processing helix chain '2' and resid 533 through 544 Processing helix chain '2' and resid 549 through 554 Processing helix chain '2' and resid 568 through 576 removed outlier: 3.632A pdb=" N PHE 2 575 " --> pdb=" O LEU 2 571 " (cutoff:3.500A) Processing helix chain '2' and resid 612 through 616 Processing helix chain '2' and resid 632 through 639 removed outlier: 5.078A pdb=" N GLN 2 637 " --> pdb=" O ILE 2 634 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR 2 639 " --> pdb=" O MET 2 636 " (cutoff:3.500A) Processing helix chain '2' and resid 692 through 702 removed outlier: 3.764A pdb=" N THR 2 696 " --> pdb=" O ALA 2 692 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 194 No H-bonds generated for 'chain '3' and resid 192 through 194' Processing helix chain '3' and resid 199 through 203 Processing helix chain '3' and resid 430 through 432 No H-bonds generated for 'chain '3' and resid 430 through 432' Processing helix chain '3' and resid 809 through 826 removed outlier: 3.572A pdb=" N VAL 3 824 " --> pdb=" O ALA 3 820 " (cutoff:3.500A) Processing helix chain '3' and resid 835 through 844 Processing helix chain '3' and resid 849 through 852 No H-bonds generated for 'chain '3' and resid 849 through 852' Processing helix chain '3' and resid 1135 through 1151 removed outlier: 3.951A pdb=" N SER 31150 " --> pdb=" O MET 31146 " (cutoff:3.500A) Processing helix chain '3' and resid 1160 through 1163 No H-bonds generated for 'chain '3' and resid 1160 through 1163' Processing helix chain '3' and resid 1176 through 1182 removed outlier: 3.733A pdb=" N GLN 31181 " --> pdb=" O ASP 31177 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE 31182 " --> pdb=" O LEU 31178 " (cutoff:3.500A) Processing helix chain '3' and resid 1187 through 1196 removed outlier: 4.086A pdb=" N GLU 31196 " --> pdb=" O ASN 31192 " (cutoff:3.500A) Processing helix chain '3' and resid 1201 through 1215 removed outlier: 3.779A pdb=" N ILE 31211 " --> pdb=" O LYS 31207 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG 31212 " --> pdb=" O LEU 31208 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 34 Processing helix chain '4' and resid 64 through 76 removed outlier: 4.255A pdb=" N ILE 4 71 " --> pdb=" O ALA 4 67 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS 4 72 " --> pdb=" O ASP 4 68 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN 4 75 " --> pdb=" O ILE 4 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET 4 76 " --> pdb=" O LYS 4 72 " (cutoff:3.500A) Processing helix chain '5' and resid 32 through 39 Processing helix chain '5' and resid 67 through 77 Processing helix chain '5' and resid 103 through 117 Processing helix chain '6' and resid 24 through 26 No H-bonds generated for 'chain '6' and resid 24 through 26' Processing helix chain '6' and resid 47 through 50 Processing helix chain '6' and resid 52 through 54 No H-bonds generated for 'chain '6' and resid 52 through 54' Processing helix chain '6' and resid 73 through 77 Processing helix chain '6' and resid 80 through 82 No H-bonds generated for 'chain '6' and resid 80 through 82' Processing helix chain '6' and resid 92 through 105 removed outlier: 3.558A pdb=" N THR 6 96 " --> pdb=" O GLY 6 92 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 17 Processing helix chain '7' and resid 28 through 45 Processing helix chain '7' and resid 47 through 56 Processing helix chain '7' and resid 61 through 71 Processing helix chain 'h' and resid 5 through 13 Processing helix chain 'h' and resid 65 through 67 No H-bonds generated for 'chain 'h' and resid 65 through 67' Processing helix chain 'i' and resid 7 through 12 removed outlier: 4.671A pdb=" N HIS i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 76 No H-bonds generated for 'chain 'i' and resid 74 through 76' Processing helix chain 'j' and resid 3 through 10 removed outlier: 3.955A pdb=" N LEU j 10 " --> pdb=" O PHE j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 62 through 64 No H-bonds generated for 'chain 'j' and resid 62 through 64' Processing helix chain 'j' and resid 76 through 80 Processing helix chain 'k' and resid 21 through 26 Processing helix chain 'k' and resid 28 through 38 removed outlier: 3.637A pdb=" N GLN k 34 " --> pdb=" O VAL k 31 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL k 36 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS k 37 " --> pdb=" O GLN k 34 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN k 38 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 103 through 105 No H-bonds generated for 'chain 'k' and resid 103 through 105' Processing helix chain 'l' and resid 17 through 27 Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' Processing helix chain 'm' and resid 7 through 14 Processing helix chain 'm' and resid 66 through 68 No H-bonds generated for 'chain 'm' and resid 66 through 68' Processing helix chain 'n' and resid 10 through 12 No H-bonds generated for 'chain 'n' and resid 10 through 12' Processing helix chain 'n' and resid 64 through 66 No H-bonds generated for 'chain 'n' and resid 64 through 66' Processing helix chain 'v' and resid 10 through 28 removed outlier: 4.145A pdb=" N TYR v 28 " --> pdb=" O LEU v 24 " (cutoff:3.500A) Processing helix chain 'v' and resid 56 through 63 Processing helix chain 'v' and resid 66 through 73 Processing helix chain 'v' and resid 184 through 198 Processing sheet with id= A, first strand: chain '3' and resid 1173 through 1175 removed outlier: 6.780A pdb=" N LEU 3 3 " --> pdb=" O ILE 31174 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE 31126 " --> pdb=" O LEU 3 8 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLU 31115 " --> pdb=" O PRO 31131 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER 31103 " --> pdb=" O THR 31120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '3' and resid 16 through 20 removed outlier: 6.361A pdb=" N ARG 3 42 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR 3 52 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '3' and resid 62 through 68 removed outlier: 6.936A pdb=" N GLY 3 81 " --> pdb=" O ARG 3 63 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU 3 65 " --> pdb=" O VAL 3 79 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL 3 79 " --> pdb=" O LEU 3 65 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA 3 67 " --> pdb=" O TYR 3 77 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR 3 77 " --> pdb=" O ALA 3 67 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER 3 82 " --> pdb=" O ARG 3 86 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG 3 86 " --> pdb=" O SER 3 82 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU 3 91 " --> pdb=" O LYS 3 101 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LYS 3 101 " --> pdb=" O GLU 3 91 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLN 3 93 " --> pdb=" O PHE 3 99 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE 3 99 " --> pdb=" O GLN 3 93 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 120 through 123 Processing sheet with id= E, first strand: chain '3' and resid 144 through 146 Processing sheet with id= F, first strand: chain '3' and resid 165 through 167 removed outlier: 6.564A pdb=" N GLU 3 212 " --> pdb=" O ARG 3 222 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG 3 222 " --> pdb=" O GLU 3 212 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP 3 214 " --> pdb=" O VAL 3 220 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL 3 220 " --> pdb=" O ASP 3 214 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 170 through 173 removed outlier: 4.477A pdb=" N MET 3 181 " --> pdb=" O VAL 3 173 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 267 through 270 removed outlier: 3.741A pdb=" N PHE 3 234 " --> pdb=" O CYS 3 251 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 287 through 294 removed outlier: 6.906A pdb=" N GLN 3 304 " --> pdb=" O VAL 3 288 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER 3 290 " --> pdb=" O LEU 3 302 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU 3 302 " --> pdb=" O SER 3 290 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR 3 292 " --> pdb=" O PHE 3 300 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE 3 300 " --> pdb=" O THR 3 292 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE 3 299 " --> pdb=" O LEU 3 315 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU 3 315 " --> pdb=" O PHE 3 299 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP 3 309 " --> pdb=" O THR 3 305 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS 3 312 " --> pdb=" O TYR 3 329 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TYR 3 329 " --> pdb=" O LYS 3 312 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR 3 314 " --> pdb=" O LEU 3 327 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU 3 327 " --> pdb=" O THR 3 314 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU 3 316 " --> pdb=" O ILE 3 325 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE 3 325 " --> pdb=" O GLU 3 316 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 336 through 342 removed outlier: 7.093A pdb=" N ALA 3 350 " --> pdb=" O ALA 3 337 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET 3 339 " --> pdb=" O PHE 3 348 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE 3 348 " --> pdb=" O MET 3 339 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL 3 341 " --> pdb=" O PHE 3 346 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE 3 346 " --> pdb=" O VAL 3 341 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN 3 360 " --> pdb=" O LEU 3 397 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU 3 397 " --> pdb=" O GLN 3 360 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 774 through 780 Processing sheet with id= L, first strand: chain '3' and resid 482 through 486 removed outlier: 3.546A pdb=" N ALA 3 458 " --> pdb=" O SER 3 477 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 533 through 537 Processing sheet with id= N, first strand: chain '3' and resid 574 through 576 removed outlier: 3.755A pdb=" N GLU 3 562 " --> pdb=" O LEU 3 558 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS 3 546 " --> pdb=" O ALA 3 557 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '3' and resid 587 through 592 removed outlier: 6.960A pdb=" N GLY 3 608 " --> pdb=" O VAL 3 588 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET 3 590 " --> pdb=" O ALA 3 606 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA 3 606 " --> pdb=" O MET 3 590 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU 3 592 " --> pdb=" O PHE 3 604 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N PHE 3 604 " --> pdb=" O LEU 3 592 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER 3 629 " --> pdb=" O ILE 3 616 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER 3 618 " --> pdb=" O PRO 3 627 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '3' and resid 689 through 693 removed outlier: 3.941A pdb=" N ARG 3 676 " --> pdb=" O ARG 3 690 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL 3 673 " --> pdb=" O LEU 3 669 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU 3 669 " --> pdb=" O VAL 3 673 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET 3 645 " --> pdb=" O PHE 3 662 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER 3 639 " --> pdb=" O GLY 3 668 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '3' and resid 700 through 703 Processing sheet with id= R, first strand: chain '3' and resid 741 through 745 removed outlier: 3.743A pdb=" N ALA 3 448 " --> pdb=" O ILE 3 764 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA 3 766 " --> pdb=" O GLU 3 446 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLU 3 446 " --> pdb=" O ALA 3 766 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '3' and resid 784 through 790 removed outlier: 3.587A pdb=" N THR 3 784 " --> pdb=" O THR 3 802 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE 3 800 " --> pdb=" O ARG 3 786 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE 3 788 " --> pdb=" O ILE 3 798 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE 3 798 " --> pdb=" O PHE 3 788 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE 3 790 " --> pdb=" O ASN 3 796 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN 3 796 " --> pdb=" O ILE 3 790 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN 3 870 " --> pdb=" O THR 3 876 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR 3 876 " --> pdb=" O ASN 3 870 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '3' and resid 886 through 895 removed outlier: 6.566A pdb=" N GLY 3 908 " --> pdb=" O PHE 3 889 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL 3 891 " --> pdb=" O LEU 3 906 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU 3 906 " --> pdb=" O VAL 3 891 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL 3 893 " --> pdb=" O TYR 3 904 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TYR 3 904 " --> pdb=" O VAL 3 893 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP 3 903 " --> pdb=" O LEU 3 930 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS 3 941 " --> pdb=" O THR 3 927 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS 3 929 " --> pdb=" O PHE 3 939 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N PHE 3 939 " --> pdb=" O LYS 3 929 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL 3 931 " --> pdb=" O LEU 3 937 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU 3 937 " --> pdb=" O VAL 3 931 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '3' and resid 977 through 980 removed outlier: 3.869A pdb=" N ALA 3 951 " --> pdb=" O GLY 3 962 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '3' and resid 990 through 996 removed outlier: 6.491A pdb=" N SER 31003 " --> pdb=" O SER 3 991 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE 3 993 " --> pdb=" O ILE 31001 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE 31001 " --> pdb=" O ILE 3 993 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR 3 995 " --> pdb=" O ARG 3 999 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG 3 999 " --> pdb=" O THR 3 995 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG 31013 " --> pdb=" O ILE 31023 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE 31023 " --> pdb=" O ARG 31013 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS 31015 " --> pdb=" O LEU 31021 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU 31021 " --> pdb=" O LYS 31015 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '3' and resid 1033 through 1038 removed outlier: 6.788A pdb=" N ALA 31047 " --> pdb=" O THR 31034 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA 31036 " --> pdb=" O ALA 31045 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA 31045 " --> pdb=" O ALA 31036 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU 31038 " --> pdb=" O THR 31043 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR 31043 " --> pdb=" O LEU 31038 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN 31052 " --> pdb=" O ASP 31048 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG 31057 " --> pdb=" O VAL 31091 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL 31091 " --> pdb=" O ARG 31057 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '4' and resid 41 through 44 Processing sheet with id= Y, first strand: chain '5' and resid 88 through 91 Processing sheet with id= Z, first strand: chain '6' and resid 39 through 42 removed outlier: 6.303A pdb=" N TYR 6 71 " --> pdb=" O CYS 6 40 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'h' and resid 55 through 58 Processing sheet with id= AB, first strand: chain 'h' and resid 60 through 63 removed outlier: 6.830A pdb=" N SER h 44 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU h 32 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'i' and resid 64 through 68 removed outlier: 6.215A pdb=" N CYS i 45 " --> pdb=" O LEU i 67 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG i 18 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL i 82 " --> pdb=" O ARG i 18 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE i 20 " --> pdb=" O MET i 80 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N MET i 80 " --> pdb=" O ILE i 20 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'i' and resid 70 through 72 removed outlier: 3.687A pdb=" N ALA i 33 " --> pdb=" O ILE i 41 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS i 43 " --> pdb=" O PHE i 31 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE i 31 " --> pdb=" O CYS i 43 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'j' and resid 53 through 55 Processing sheet with id= AF, first strand: chain 'j' and resid 57 through 60 removed outlier: 6.030A pdb=" N LYS j 41 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE j 29 " --> pdb=" O LYS j 41 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'k' and resid 90 through 96 Processing sheet with id= AH, first strand: chain 'k' and resid 98 through 101 removed outlier: 6.580A pdb=" N GLU k 68 " --> pdb=" O VAL k 56 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL k 56 " --> pdb=" O GLU k 68 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'l' and resid 70 through 75 removed outlier: 5.721A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG l 30 " --> pdb=" O VAL l 90 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'l' and resid 77 through 79 removed outlier: 3.790A pdb=" N GLY l 49 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP l 59 " --> pdb=" O ILE l 47 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE l 47 " --> pdb=" O ASP l 59 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'm' and resid 57 through 60 removed outlier: 3.571A pdb=" N GLY m 57 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR m 47 " --> pdb=" O LEU m 59 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'm' and resid 62 through 64 removed outlier: 3.670A pdb=" N SER m 35 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA m 45 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU m 33 " --> pdb=" O ALA m 45 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'n' and resid 67 through 72 removed outlier: 6.920A pdb=" N LYS n 20 " --> pdb=" O ILE n 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU n 70 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER n 18 " --> pdb=" O LEU n 70 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA n 72 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LYS n 16 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'n' and resid 45 through 47 removed outlier: 6.476A pdb=" N GLU n 47 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASN n 56 " --> pdb=" O GLU n 47 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'v' and resid 34 through 36 1034 hydrogen bonds defined for protein. 2886 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 13.02 Time building geometry restraints manager: 11.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4640 1.31 - 1.43: 7467 1.43 - 1.56: 15073 1.56 - 1.69: 202 1.69 - 1.81: 200 Bond restraints: 27582 Sorted by residual: bond pdb=" C THR 3 784 " pdb=" N PRO 3 785 " ideal model delta sigma weight residual 1.333 1.281 0.053 1.01e-02 9.80e+03 2.74e+01 bond pdb=" OG1 TPO 3 613 " pdb=" P TPO 3 613 " ideal model delta sigma weight residual 1.717 1.614 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" CA LEU m 14 " pdb=" C LEU m 14 " ideal model delta sigma weight residual 1.522 1.592 -0.070 1.37e-02 5.33e+03 2.61e+01 bond pdb=" CA MET k 73 " pdb=" C MET k 73 " ideal model delta sigma weight residual 1.521 1.461 0.060 1.24e-02 6.50e+03 2.36e+01 bond pdb=" CG LEU 11172 " pdb=" CD1 LEU 11172 " ideal model delta sigma weight residual 1.521 1.366 0.155 3.30e-02 9.18e+02 2.22e+01 ... (remaining 27577 not shown) Histogram of bond angle deviations from ideal: 92.43 - 101.18: 92 101.18 - 109.92: 7016 109.92 - 118.67: 15550 118.67 - 127.42: 14791 127.42 - 136.17: 359 Bond angle restraints: 37808 Sorted by residual: angle pdb=" N ILE 6 60 " pdb=" CA ILE 6 60 " pdb=" C ILE 6 60 " ideal model delta sigma weight residual 110.62 119.46 -8.84 1.02e+00 9.61e-01 7.50e+01 angle pdb=" C PRO 2 642 " pdb=" N PRO 2 643 " pdb=" CA PRO 2 643 " ideal model delta sigma weight residual 119.05 128.21 -9.16 1.11e+00 8.12e-01 6.81e+01 angle pdb=" N ARG 11262 " pdb=" CA ARG 11262 " pdb=" C ARG 11262 " ideal model delta sigma weight residual 111.07 118.95 -7.88 1.07e+00 8.73e-01 5.42e+01 angle pdb=" N CYS 3 981 " pdb=" CA CYS 3 981 " pdb=" C CYS 3 981 " ideal model delta sigma weight residual 111.39 120.96 -9.57 1.38e+00 5.25e-01 4.81e+01 angle pdb=" N LYS 3 137 " pdb=" CA LYS 3 137 " pdb=" C LYS 3 137 " ideal model delta sigma weight residual 112.86 120.88 -8.02 1.22e+00 6.72e-01 4.32e+01 ... (remaining 37803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 16248 33.80 - 67.60: 479 67.60 - 101.40: 30 101.40 - 135.20: 2 135.20 - 169.00: 2 Dihedral angle restraints: 16761 sinusoidal: 6849 harmonic: 9912 Sorted by residual: dihedral pdb=" O4' U A 222 " pdb=" C1' U A 222 " pdb=" N1 U A 222 " pdb=" C2 U A 222 " ideal model delta sinusoidal sigma weight residual -160.00 -52.36 -107.64 1 1.50e+01 4.44e-03 5.56e+01 dihedral pdb=" CA LEU m 3 " pdb=" C LEU m 3 " pdb=" N PRO m 4 " pdb=" CA PRO m 4 " ideal model delta harmonic sigma weight residual -180.00 -150.24 -29.76 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA LYS m 17 " pdb=" C LYS m 17 " pdb=" N PRO m 18 " pdb=" CA PRO m 18 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 16758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3178 0.093 - 0.185: 1003 0.185 - 0.278: 180 0.278 - 0.370: 26 0.370 - 0.463: 6 Chirality restraints: 4393 Sorted by residual: chirality pdb=" CB VAL 2 498 " pdb=" CA VAL 2 498 " pdb=" CG1 VAL 2 498 " pdb=" CG2 VAL 2 498 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA CYS 3 981 " pdb=" N CYS 3 981 " pdb=" C CYS 3 981 " pdb=" CB CYS 3 981 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CB THR 11113 " pdb=" CA THR 11113 " pdb=" OG1 THR 11113 " pdb=" CG2 THR 11113 " both_signs ideal model delta sigma weight residual False 2.55 2.13 0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 4390 not shown) Planarity restraints: 4668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U H 79 " 0.073 2.00e-02 2.50e+03 3.50e-02 2.75e+01 pdb=" N1 U H 79 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U H 79 " -0.010 2.00e-02 2.50e+03 pdb=" O2 U H 79 " -0.018 2.00e-02 2.50e+03 pdb=" N3 U H 79 " -0.012 2.00e-02 2.50e+03 pdb=" C4 U H 79 " 0.011 2.00e-02 2.50e+03 pdb=" O4 U H 79 " 0.035 2.00e-02 2.50e+03 pdb=" C5 U H 79 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U H 79 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G H 81 " 0.048 2.00e-02 2.50e+03 2.78e-02 2.33e+01 pdb=" N9 G H 81 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G H 81 " -0.010 2.00e-02 2.50e+03 pdb=" N7 G H 81 " -0.011 2.00e-02 2.50e+03 pdb=" C5 G H 81 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G H 81 " 0.022 2.00e-02 2.50e+03 pdb=" O6 G H 81 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G H 81 " 0.032 2.00e-02 2.50e+03 pdb=" C2 G H 81 " -0.062 2.00e-02 2.50e+03 pdb=" N2 G H 81 " 0.013 2.00e-02 2.50e+03 pdb=" N3 G H 81 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G H 81 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 2 575 " -0.026 2.00e-02 2.50e+03 3.33e-02 1.94e+01 pdb=" CG PHE 2 575 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE 2 575 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE 2 575 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE 2 575 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE 2 575 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE 2 575 " 0.003 2.00e-02 2.50e+03 ... (remaining 4665 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 521 2.64 - 3.20: 23904 3.20 - 3.77: 41576 3.77 - 4.33: 55018 4.33 - 4.90: 92146 Nonbonded interactions: 213165 Sorted by model distance: nonbonded pdb=" O2' C A 206 " pdb=" OP2 A A 207 " model vdw 2.073 2.440 nonbonded pdb=" O SER 11276 " pdb=" OG SER 11276 " model vdw 2.191 2.440 nonbonded pdb=" CE2 PHE 2 694 " pdb=" OD1 ASP v 191 " model vdw 2.221 3.340 nonbonded pdb=" O2' U A 211 " pdb=" OP2 C A 213 " model vdw 2.246 2.440 nonbonded pdb=" NH2 ARG v 5 " pdb=" O GLY v 7 " model vdw 2.253 2.520 ... (remaining 213160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 9.220 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: 0.030 Extract box with map and model: 28.910 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 85.680 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0973 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 : 0.023 0.184 27582 Z= 1.526 Angle : 1.393 12.016 37808 Z= 0.824 Chirality : 0.091 0.463 4393 Planarity : 0.009 0.091 4668 Dihedral : 15.108 168.999 10355 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.83 % Allowed : 5.63 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: -1.68 (0.13), residues: 3364 helix: -1.58 (0.13), residues: 1068 sheet: -0.37 (0.18), residues: 740 loop : -0.99 (0.14), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP 7 31 HIS 0.020 0.005 HIS 11194 PHE 0.076 0.006 PHE 2 575 TYR 0.062 0.005 TYR 6 36 ARG 0.025 0.003 ARG 1 924 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 156 time to evaluate : 2.737 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: 1 126 MET cc_start: -0.3946 (mtm) cc_final: -0.4214 (mtm) REVERT: 1 147 MET cc_start: 0.0710 (tpp) cc_final: 0.0443 (ttt) REVERT: 1 656 LYS cc_start: 0.2345 (mmpt) cc_final: 0.0818 (pttt) REVERT: 1 675 MET cc_start: -0.0036 (OUTLIER) cc_final: -0.0775 (mmt) REVERT: 1 976 VAL cc_start: -0.5644 (OUTLIER) cc_final: -0.5859 (t) REVERT: 1 1112 THR cc_start: 0.3175 (OUTLIER) cc_final: 0.2957 (p) REVERT: 2 579 GLN cc_start: -0.2624 (OUTLIER) cc_final: -0.3094 (tt0) REVERT: 3 339 MET cc_start: 0.1397 (mtm) cc_final: 0.0826 (mmt) REVERT: 3 1146 MET cc_start: -0.0162 (mtm) cc_final: -0.1035 (ttp) REVERT: 3 1185 MET cc_start: -0.1241 (mtm) cc_final: -0.2128 (tpt) REVERT: 7 1 MET cc_start: 0.3840 (ttt) cc_final: 0.2945 (mtt) outliers start: 92 outliers final: 14 residues processed: 243 average time/residue: 0.4253 time to fit residues: 161.1915 Evaluate side-chains 148 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 50.0000 chunk 259 optimal weight: 30.0000 chunk 144 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 175 optimal weight: 40.0000 chunk 138 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 104 optimal weight: 30.0000 chunk 163 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 overall best weight: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 473 GLN 1 547 GLN 1 659 GLN 1 804 ASN 1 829 ASN 1 901 GLN 1 912 ASN ** 11108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11277 GLN 2 579 GLN ** 2 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 51 HIS ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 440 HIS 3 612 ASN 5 84 ASN ** 6 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1075 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27582 Z= 0.192 Angle : 0.590 8.364 37808 Z= 0.316 Chirality : 0.043 0.178 4393 Planarity : 0.005 0.055 4668 Dihedral : 12.996 158.089 4890 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.04 % Allowed : 2.17 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: -0.38 (0.14), residues: 3364 helix: 0.06 (0.15), residues: 1066 sheet: -0.09 (0.19), residues: 695 loop : -0.40 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 2 578 HIS 0.006 0.001 HIS 1 682 PHE 0.013 0.002 PHE 31217 TYR 0.023 0.002 TYR 1 830 ARG 0.006 0.001 ARG 2 495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1177 (tpp) cc_final: 0.0580 (ttt) REVERT: 1 511 MET cc_start: 0.3708 (mmp) cc_final: 0.3143 (mmt) REVERT: 1 609 MET cc_start: -0.1384 (mmt) cc_final: -0.2798 (tmm) REVERT: 1 620 MET cc_start: 0.3285 (tmm) cc_final: 0.2198 (ttm) REVERT: 1 656 LYS cc_start: 0.2853 (mmpt) cc_final: 0.1443 (pttt) REVERT: 1 867 MET cc_start: 0.3150 (tpt) cc_final: 0.2526 (tpt) REVERT: 1 1178 MET cc_start: 0.5206 (ptm) cc_final: 0.4619 (ptm) REVERT: 3 339 MET cc_start: 0.1521 (mtm) cc_final: 0.1200 (mmm) REVERT: 3 380 GLU cc_start: 0.7428 (pp20) cc_final: 0.7047 (pp20) REVERT: 3 1146 MET cc_start: -0.0055 (mtm) cc_final: -0.0761 (ttp) REVERT: 3 1185 MET cc_start: -0.1732 (mtm) cc_final: -0.2431 (tpt) REVERT: v 1 MET cc_start: 0.4020 (mpp) cc_final: 0.3793 (mpp) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.3395 time to fit residues: 81.8637 Evaluate side-chains 127 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 30.0000 chunk 96 optimal weight: 50.0000 chunk 259 optimal weight: 30.0000 chunk 212 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 312 optimal weight: 2.9990 chunk 337 optimal weight: 30.0000 chunk 277 optimal weight: 60.0000 chunk 309 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 250 optimal weight: 20.0000 overall best weight: 9.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 804 ASN ** 1 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11209 ASN 11277 GLN 2 496 ASN ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1130 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 27582 Z= 0.159 Angle : 0.516 9.263 37808 Z= 0.273 Chirality : 0.042 0.210 4393 Planarity : 0.004 0.061 4668 Dihedral : 12.768 171.364 4890 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: 0.15 (0.14), residues: 3364 helix: 0.77 (0.16), residues: 1067 sheet: -0.02 (0.19), residues: 712 loop : -0.18 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP v 201 HIS 0.005 0.001 HIS 7 36 PHE 0.015 0.001 PHE v 42 TYR 0.021 0.001 TYR 1 805 ARG 0.007 0.000 ARG 1 495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.916 Fit side-chains revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1248 (tpp) cc_final: 0.0119 (ttt) REVERT: 1 156 MET cc_start: -0.1664 (mmm) cc_final: -0.2277 (ptp) REVERT: 1 511 MET cc_start: 0.3667 (mmp) cc_final: 0.2954 (mmt) REVERT: 1 609 MET cc_start: -0.1649 (mmt) cc_final: -0.2782 (tmm) REVERT: 1 620 MET cc_start: 0.3203 (tmm) cc_final: 0.1989 (ttm) REVERT: 1 656 LYS cc_start: 0.2954 (mmpt) cc_final: 0.1187 (pttt) REVERT: 1 867 MET cc_start: 0.4085 (tpt) cc_final: 0.3351 (tpt) REVERT: 1 1178 MET cc_start: 0.5075 (ptm) cc_final: 0.4462 (ptm) REVERT: 2 694 PHE cc_start: 0.3926 (t80) cc_final: 0.3462 (t80) REVERT: 3 339 MET cc_start: 0.1776 (mtm) cc_final: 0.1478 (mmm) REVERT: 3 1146 MET cc_start: -0.0463 (mtm) cc_final: -0.0753 (ttp) REVERT: 3 1185 MET cc_start: -0.1107 (mtm) cc_final: -0.2119 (tpt) REVERT: 5 26 LEU cc_start: 0.4724 (mm) cc_final: 0.4219 (mt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3542 time to fit residues: 81.2464 Evaluate side-chains 124 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 50.0000 chunk 234 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 34 optimal weight: 50.0000 chunk 148 optimal weight: 40.0000 chunk 209 optimal weight: 0.0970 chunk 313 optimal weight: 0.0970 chunk 331 optimal weight: 40.0000 chunk 163 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11209 ASN ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 304 GLN ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1111 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27582 Z= 0.113 Angle : 0.470 9.153 37808 Z= 0.247 Chirality : 0.041 0.202 4393 Planarity : 0.004 0.053 4668 Dihedral : 12.691 168.251 4890 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: 0.42 (0.14), residues: 3364 helix: 1.08 (0.16), residues: 1076 sheet: 0.09 (0.19), residues: 741 loop : -0.07 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 31011 HIS 0.002 0.000 HIS v 192 PHE 0.013 0.001 PHE 11155 TYR 0.019 0.001 TYR 5 61 ARG 0.002 0.000 ARG 3 705 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.057 Fit side-chains revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1291 (tpp) cc_final: 0.0104 (ttt) REVERT: 1 156 MET cc_start: -0.1596 (mmm) cc_final: -0.2280 (ptm) REVERT: 1 511 MET cc_start: 0.3283 (mmp) cc_final: 0.2603 (mmt) REVERT: 1 609 MET cc_start: -0.1984 (mmt) cc_final: -0.2973 (tmm) REVERT: 1 620 MET cc_start: 0.3326 (tmm) cc_final: 0.2051 (ttm) REVERT: 1 656 LYS cc_start: 0.2312 (mmpt) cc_final: 0.0742 (pttt) REVERT: 1 867 MET cc_start: 0.3444 (tpt) cc_final: 0.2795 (tpt) REVERT: 1 876 MET cc_start: 0.4105 (mtt) cc_final: 0.3879 (mtt) REVERT: 1 962 MET cc_start: -0.0253 (mmm) cc_final: -0.0768 (mmm) REVERT: 1 1178 MET cc_start: 0.4962 (ptm) cc_final: 0.4361 (ptm) REVERT: 2 653 LEU cc_start: 0.2388 (tp) cc_final: 0.2176 (tt) REVERT: 3 339 MET cc_start: 0.1786 (mtm) cc_final: 0.1549 (mmm) REVERT: 3 447 MET cc_start: 0.0646 (mmm) cc_final: -0.0997 (mtt) REVERT: 3 1185 MET cc_start: -0.0781 (mtm) cc_final: -0.1487 (tpt) REVERT: 5 26 LEU cc_start: 0.4722 (mm) cc_final: 0.4224 (mt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3395 time to fit residues: 77.9628 Evaluate side-chains 121 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 60.0000 chunk 188 optimal weight: 40.0000 chunk 4 optimal weight: 50.0000 chunk 246 optimal weight: 7.9990 chunk 136 optimal weight: 20.0000 chunk 282 optimal weight: 9.9990 chunk 229 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 169 optimal weight: 9.9990 chunk 297 optimal weight: 50.0000 chunk 83 optimal weight: 30.0000 overall best weight: 15.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 804 ASN 1 817 HIS ** 1 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11034 ASN 11108 ASN 11184 HIS ** 11252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 569 GLN 2 572 HIS ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 709 GLN 31192 ASN ** 7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1302 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27582 Z= 0.214 Angle : 0.642 15.869 37808 Z= 0.334 Chirality : 0.045 0.237 4393 Planarity : 0.005 0.056 4668 Dihedral : 13.046 177.212 4890 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: 0.10 (0.14), residues: 3364 helix: 0.71 (0.16), residues: 1060 sheet: 0.01 (0.20), residues: 699 loop : -0.23 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 3 460 HIS 0.009 0.002 HIS 31138 PHE 0.020 0.002 PHE 3 385 TYR 0.033 0.002 TYR 1 830 ARG 0.011 0.001 ARG 3 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.926 Fit side-chains REVERT: 1 147 MET cc_start: 0.1398 (tpp) cc_final: -0.0164 (ttt) REVERT: 1 511 MET cc_start: 0.3508 (mmp) cc_final: 0.3017 (mmp) REVERT: 1 609 MET cc_start: -0.1706 (mmt) cc_final: -0.2393 (tmm) REVERT: 1 656 LYS cc_start: 0.2198 (mmpt) cc_final: 0.0083 (pttp) REVERT: 1 867 MET cc_start: 0.4473 (tpt) cc_final: 0.3351 (tpt) REVERT: 1 876 MET cc_start: 0.3400 (mtt) cc_final: 0.3138 (mtt) REVERT: 1 1178 MET cc_start: 0.5130 (ptm) cc_final: 0.4445 (ptm) REVERT: 2 526 ASP cc_start: 0.6688 (p0) cc_final: 0.6329 (p0) REVERT: 3 339 MET cc_start: 0.3107 (mtm) cc_final: 0.2330 (mmt) REVERT: 3 1185 MET cc_start: -0.0688 (mtm) cc_final: -0.1240 (tpt) REVERT: 5 26 LEU cc_start: 0.4923 (mm) cc_final: 0.4498 (mm) REVERT: 5 92 TYR cc_start: 0.1946 (t80) cc_final: 0.1548 (t80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.3413 time to fit residues: 77.1995 Evaluate side-chains 120 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 50.0000 chunk 298 optimal weight: 20.0000 chunk 65 optimal weight: 0.1980 chunk 194 optimal weight: 50.0000 chunk 81 optimal weight: 8.9990 chunk 331 optimal weight: 30.0000 chunk 275 optimal weight: 50.0000 chunk 153 optimal weight: 50.0000 chunk 27 optimal weight: 50.0000 chunk 109 optimal weight: 40.0000 chunk 174 optimal weight: 10.0000 overall best weight: 13.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 599 ASN 11225 HIS ** 11256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 458 ASN ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1303 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27582 Z= 0.156 Angle : 0.524 9.130 37808 Z= 0.275 Chirality : 0.042 0.213 4393 Planarity : 0.004 0.060 4668 Dihedral : 12.997 175.838 4890 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.04 % Allowed : 1.42 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: 0.14 (0.14), residues: 3364 helix: 0.83 (0.16), residues: 1075 sheet: -0.14 (0.19), residues: 698 loop : -0.20 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 819 HIS 0.005 0.001 HIS 11194 PHE 0.014 0.001 PHE 1 632 TYR 0.017 0.001 TYR 1 764 ARG 0.006 0.000 ARG 3 525 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1415 (tpp) cc_final: -0.0273 (ttt) REVERT: 1 156 MET cc_start: -0.2463 (mmt) cc_final: -0.3538 (ptm) REVERT: 1 511 MET cc_start: 0.2903 (mmp) cc_final: 0.2468 (mmp) REVERT: 1 540 MET cc_start: -0.2998 (mmt) cc_final: -0.3563 (tpp) REVERT: 1 609 MET cc_start: -0.1788 (mmt) cc_final: -0.2269 (tmm) REVERT: 1 656 LYS cc_start: 0.1401 (mmpt) cc_final: -0.0783 (pttp) REVERT: 1 867 MET cc_start: 0.3933 (tpt) cc_final: 0.3234 (tpt) REVERT: 1 1178 MET cc_start: 0.5503 (ptm) cc_final: 0.4837 (ptm) REVERT: 2 526 ASP cc_start: 0.6840 (p0) cc_final: 0.6504 (p0) REVERT: 3 447 MET cc_start: 0.1097 (mmm) cc_final: -0.0021 (mtt) REVERT: 3 869 MET cc_start: 0.0101 (ppp) cc_final: -0.3172 (ptp) REVERT: 3 1185 MET cc_start: -0.0473 (mtm) cc_final: -0.0784 (tpt) REVERT: 5 101 MET cc_start: 0.3540 (pmm) cc_final: 0.3335 (pmm) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.3344 time to fit residues: 76.7470 Evaluate side-chains 121 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 242 optimal weight: 50.0000 chunk 187 optimal weight: 50.0000 chunk 279 optimal weight: 50.0000 chunk 185 optimal weight: 50.0000 chunk 330 optimal weight: 0.0000 chunk 206 optimal weight: 3.9990 chunk 201 optimal weight: 40.0000 chunk 152 optimal weight: 8.9990 overall best weight: 5.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 11256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 103 HIS ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1284 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27582 Z= 0.122 Angle : 0.482 9.252 37808 Z= 0.253 Chirality : 0.041 0.207 4393 Planarity : 0.004 0.057 4668 Dihedral : 12.888 173.091 4890 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: 0.37 (0.15), residues: 3364 helix: 1.09 (0.16), residues: 1080 sheet: -0.10 (0.19), residues: 713 loop : -0.06 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 1 732 HIS 0.005 0.001 HIS 3 169 PHE 0.012 0.001 PHE 1 632 TYR 0.016 0.001 TYR 1 830 ARG 0.004 0.000 ARG 3 615 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1106 (tpp) cc_final: -0.0495 (ttt) REVERT: 1 446 MET cc_start: 0.3169 (mpp) cc_final: -0.0785 (ppp) REVERT: 1 540 MET cc_start: -0.3097 (mmt) cc_final: -0.3625 (tpp) REVERT: 1 620 MET cc_start: 0.4955 (tmm) cc_final: 0.3185 (mtt) REVERT: 1 867 MET cc_start: 0.4050 (tpt) cc_final: 0.3360 (tpt) REVERT: 1 1178 MET cc_start: 0.5140 (ptm) cc_final: 0.4614 (ptm) REVERT: 2 526 ASP cc_start: 0.6941 (p0) cc_final: 0.6563 (p0) REVERT: 3 447 MET cc_start: 0.0921 (mmm) cc_final: -0.0262 (mtt) REVERT: 3 583 MET cc_start: -0.4013 (mtt) cc_final: -0.4329 (mtt) REVERT: 3 1185 MET cc_start: -0.0502 (mtm) cc_final: -0.0744 (tpt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.3615 time to fit residues: 80.5362 Evaluate side-chains 120 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 50.0000 chunk 132 optimal weight: 50.0000 chunk 197 optimal weight: 40.0000 chunk 99 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 210 optimal weight: 30.0000 chunk 225 optimal weight: 0.0050 chunk 163 optimal weight: 40.0000 chunk 30 optimal weight: 40.0000 chunk 259 optimal weight: 8.9990 chunk 300 optimal weight: 20.0000 overall best weight: 9.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1320 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27582 Z= 0.142 Angle : 0.510 9.364 37808 Z= 0.265 Chirality : 0.041 0.210 4393 Planarity : 0.004 0.058 4668 Dihedral : 12.931 173.473 4890 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: 0.31 (0.15), residues: 3364 helix: 0.99 (0.16), residues: 1079 sheet: -0.10 (0.20), residues: 693 loop : -0.07 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP 2 578 HIS 0.007 0.001 HIS 11194 PHE 0.037 0.001 PHE 11155 TYR 0.019 0.001 TYR 1 830 ARG 0.005 0.000 ARG 1 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1178 (tpp) cc_final: -0.0534 (ttt) REVERT: 1 156 MET cc_start: -0.2216 (tpp) cc_final: -0.3530 (ptm) REVERT: 1 446 MET cc_start: 0.3176 (mpp) cc_final: -0.1011 (ppp) REVERT: 1 540 MET cc_start: -0.2898 (mmt) cc_final: -0.3252 (tpp) REVERT: 1 620 MET cc_start: 0.4873 (tmm) cc_final: 0.3223 (mtt) REVERT: 1 757 MET cc_start: -0.1222 (mmm) cc_final: -0.1483 (mmm) REVERT: 1 867 MET cc_start: 0.4142 (tpt) cc_final: 0.3229 (tpt) REVERT: 1 869 MET cc_start: -0.0556 (tmm) cc_final: -0.0930 (ttp) REVERT: 1 1178 MET cc_start: 0.5179 (ptm) cc_final: 0.4568 (ptm) REVERT: 2 526 ASP cc_start: 0.6931 (p0) cc_final: 0.6486 (p0) REVERT: 3 447 MET cc_start: 0.1329 (mmm) cc_final: -0.0025 (mtt) REVERT: 3 583 MET cc_start: -0.3971 (mtt) cc_final: -0.4180 (mtt) REVERT: 3 630 MET cc_start: 0.3130 (mmt) cc_final: 0.1862 (mmt) REVERT: 3 1185 MET cc_start: -0.0304 (mtm) cc_final: -0.0622 (tpt) REVERT: 7 69 MET cc_start: 0.0497 (mpp) cc_final: -0.0371 (ptp) REVERT: 7 72 MET cc_start: -0.1269 (ptp) cc_final: -0.1973 (ptt) REVERT: v 58 MET cc_start: 0.3050 (tpt) cc_final: 0.2448 (tpt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3359 time to fit residues: 74.7342 Evaluate side-chains 118 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 30.0000 chunk 288 optimal weight: 0.6980 chunk 308 optimal weight: 50.0000 chunk 185 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 278 optimal weight: 70.0000 chunk 291 optimal weight: 50.0000 chunk 306 optimal weight: 50.0000 chunk 202 optimal weight: 0.4980 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 5 ASN ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 103 HIS ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1298 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27582 Z= 0.121 Angle : 0.480 9.292 37808 Z= 0.248 Chirality : 0.041 0.207 4393 Planarity : 0.004 0.058 4668 Dihedral : 12.865 171.956 4890 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: 0.44 (0.15), residues: 3364 helix: 1.19 (0.16), residues: 1074 sheet: -0.13 (0.20), residues: 686 loop : -0.01 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP 2 578 HIS 0.006 0.001 HIS 11194 PHE 0.017 0.001 PHE 11155 TYR 0.019 0.001 TYR 3 577 ARG 0.006 0.000 ARG 1 702 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1118 (tpp) cc_final: -0.0578 (ttt) REVERT: 1 446 MET cc_start: 0.3065 (mpp) cc_final: -0.1045 (ppp) REVERT: 1 540 MET cc_start: -0.3170 (mmt) cc_final: -0.3481 (tpp) REVERT: 1 620 MET cc_start: 0.4941 (tmm) cc_final: 0.3549 (mtt) REVERT: 1 867 MET cc_start: 0.3681 (tpt) cc_final: 0.2959 (tpt) REVERT: 1 1178 MET cc_start: 0.5122 (ptm) cc_final: 0.4592 (ptm) REVERT: 2 526 ASP cc_start: 0.6885 (p0) cc_final: 0.6478 (p0) REVERT: 3 447 MET cc_start: 0.1334 (mmm) cc_final: 0.0082 (mtt) REVERT: 3 583 MET cc_start: -0.3919 (mtt) cc_final: -0.4362 (mtt) REVERT: 3 630 MET cc_start: 0.3140 (mmt) cc_final: 0.2094 (mmt) REVERT: 3 1185 MET cc_start: -0.0175 (mtm) cc_final: -0.0579 (tpt) REVERT: 7 69 MET cc_start: -0.0058 (mpp) cc_final: -0.0890 (mmp) REVERT: 7 72 MET cc_start: -0.0886 (ptp) cc_final: -0.1471 (ptt) REVERT: v 58 MET cc_start: 0.3040 (tpt) cc_final: 0.2300 (tpt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3654 time to fit residues: 81.8054 Evaluate side-chains 118 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 50.0000 chunk 198 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 341 optimal weight: 2.9990 chunk 314 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 210 optimal weight: 30.0000 chunk 166 optimal weight: 50.0000 chunk 216 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1314 moved from start: 0.6942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27582 Z= 0.126 Angle : 0.480 9.348 37808 Z= 0.249 Chirality : 0.041 0.210 4393 Planarity : 0.004 0.057 4668 Dihedral : 12.806 171.720 4890 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: 0.52 (0.15), residues: 3364 helix: 1.28 (0.17), residues: 1065 sheet: -0.12 (0.20), residues: 696 loop : 0.05 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 2 578 HIS 0.007 0.001 HIS 11007 PHE 0.018 0.001 PHE 11155 TYR 0.020 0.001 TYR 3 577 ARG 0.003 0.000 ARG 11245 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1109 (tpp) cc_final: -0.0822 (ttt) REVERT: 1 446 MET cc_start: 0.3034 (mpp) cc_final: -0.1059 (ppp) REVERT: 1 540 MET cc_start: -0.3016 (mmt) cc_final: -0.3349 (tpp) REVERT: 1 620 MET cc_start: 0.5091 (tmm) cc_final: 0.4145 (mtt) REVERT: 1 867 MET cc_start: 0.3883 (tpt) cc_final: 0.2780 (tpt) REVERT: 1 1178 MET cc_start: 0.5123 (ptm) cc_final: 0.4646 (ptm) REVERT: 2 526 ASP cc_start: 0.7046 (p0) cc_final: 0.6694 (p0) REVERT: 2 653 LEU cc_start: 0.2654 (tt) cc_final: 0.1891 (pt) REVERT: 3 66 MET cc_start: 0.1477 (mmp) cc_final: 0.0402 (mmp) REVERT: 3 447 MET cc_start: 0.1585 (mmm) cc_final: 0.0399 (mtt) REVERT: 3 583 MET cc_start: -0.3917 (mtt) cc_final: -0.4381 (mtt) REVERT: 3 630 MET cc_start: 0.3116 (mmt) cc_final: 0.2833 (mmt) REVERT: 3 838 MET cc_start: -0.3819 (tpt) cc_final: -0.5835 (tmm) REVERT: 3 1185 MET cc_start: -0.0037 (mtm) cc_final: -0.0393 (tpt) REVERT: 7 69 MET cc_start: 0.0092 (mpp) cc_final: -0.0321 (mmp) REVERT: 7 72 MET cc_start: -0.1106 (ptp) cc_final: -0.1717 (ptt) REVERT: v 58 MET cc_start: 0.3311 (tpt) cc_final: 0.2472 (tpt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3625 time to fit residues: 79.5854 Evaluate side-chains 118 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 250 optimal weight: 50.0000 chunk 40 optimal weight: 40.0000 chunk 75 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 114 optimal weight: 0.3980 chunk 279 optimal weight: 50.0000 chunk 34 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 chunk 239 optimal weight: 40.0000 overall best weight: 11.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.067967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.065136 restraints weight = 490907.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.063672 restraints weight = 1026560.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.062978 restraints weight = 1574248.694| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2786 moved from start: 0.7826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 27582 Z= 0.156 Angle : 0.529 9.338 37808 Z= 0.276 Chirality : 0.042 0.214 4393 Planarity : 0.004 0.058 4668 Dihedral : 12.937 173.850 4890 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: 0.30 (0.15), residues: 3364 helix: 1.11 (0.16), residues: 1056 sheet: -0.21 (0.19), residues: 710 loop : -0.11 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 2 578 HIS 0.004 0.001 HIS 7 8 PHE 0.020 0.001 PHE 1 914 TYR 0.022 0.001 TYR 3 577 ARG 0.004 0.000 ARG v 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4089.21 seconds wall clock time: 77 minutes 47.41 seconds (4667.41 seconds total)