Starting phenix.real_space_refine on Fri Aug 9 16:53:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/08_2024/8y7e_39013.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/08_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_39013/08_2024/8y7e_39013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/08_2024/8y7e_39013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/08_2024/8y7e_39013.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y7e_39013/08_2024/8y7e_39013.cif" } 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 17.72, per 1000 atoms: 0.66 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: 11.15 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... Secondary structure from input PDB file: 120 helices and 31 sheets defined 38.3% alpha, 23.0% beta 16 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 9.48 Creating SS restraints... Processing helix chain '1' and resid 102 through 107 removed outlier: 3.526A pdb=" N ALA 1 105 " --> pdb=" O ASP 1 102 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU 1 106 " --> pdb=" O PRO 1 103 " (cutoff:3.500A) Processing helix chain '1' and resid 119 through 125 removed outlier: 3.628A pdb=" N HIS 1 122 " --> pdb=" O TYR 1 119 " (cutoff:3.500A) Processing helix chain '1' and resid 136 through 141 removed outlier: 3.730A pdb=" N LYS 1 141 " --> pdb=" O ALA 1 137 " (cutoff:3.500A) Processing helix chain '1' and resid 151 through 176 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) removed outlier: 3.914A pdb=" N ALA 1 176 " --> pdb=" O LEU 1 172 " (cutoff:3.500A) Processing helix chain '1' and resid 400 through 405 removed outlier: 3.792A pdb=" N ASP 1 405 " --> pdb=" O ASP 1 401 " (cutoff:3.500A) Processing helix chain '1' and resid 406 through 408 No H-bonds generated for 'chain '1' and resid 406 through 408' Processing helix chain '1' and resid 451 through 456 Processing helix chain '1' and resid 468 through 472 removed outlier: 3.662A pdb=" N ILE 1 472 " --> pdb=" O PRO 1 469 " (cutoff:3.500A) Processing helix chain '1' and resid 475 through 479 Processing helix chain '1' and resid 488 through 507 Processing helix chain '1' and resid 508 through 522 Processing helix chain '1' and resid 522 through 527 Processing helix chain '1' and resid 527 through 540 removed outlier: 3.655A pdb=" N LEU 1 531 " --> pdb=" O GLY 1 527 " (cutoff:3.500A) 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 545 through 563 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 567 through 569 No H-bonds generated for 'chain '1' and resid 567 through 569' Processing helix chain '1' and resid 570 through 579 removed outlier: 3.870A pdb=" N VAL 1 577 " --> pdb=" O LYS 1 573 " (cutoff:3.500A) Processing helix chain '1' and resid 580 through 584 Processing helix chain '1' and resid 586 through 605 Processing helix chain '1' and resid 605 through 614 Processing helix chain '1' and resid 615 through 618 Processing helix chain '1' and resid 621 through 640 removed outlier: 3.583A pdb=" N ARG 1 625 " --> pdb=" O ASP 1 621 " (cutoff:3.500A) 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 640 through 653 removed outlier: 4.023A pdb=" N LEU 1 644 " --> pdb=" O GLY 1 640 " (cutoff:3.500A) Proline residue: 1 646 - end of helix Processing helix chain '1' and resid 657 through 676 removed outlier: 3.635A pdb=" N ARG 1 661 " --> pdb=" O SER 1 657 " (cutoff:3.500A) Processing helix chain '1' and resid 677 through 681 Proline residue: 1 681 - end of helix Processing helix chain '1' and resid 682 through 691 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) Processing helix chain '1' and resid 692 through 694 No H-bonds generated for 'chain '1' and resid 692 through 694' Processing helix chain '1' and resid 698 through 716 Processing helix chain '1' and resid 727 through 738 Processing helix chain '1' and resid 741 through 757 removed outlier: 4.352A pdb=" N ALA 1 745 " --> pdb=" O LYS 1 741 " (cutoff:3.500A) Proline residue: 1 755 - end of helix Processing helix chain '1' and resid 758 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 781 through 798 removed outlier: 3.908A pdb=" N LYS 1 790 " --> pdb=" O LYS 1 786 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR 1 798 " --> pdb=" O GLN 1 794 " (cutoff:3.500A) Processing helix chain '1' and resid 802 through 810 Processing helix chain '1' and resid 810 through 818 Processing helix chain '1' and resid 826 through 845 removed outlier: 3.742A pdb=" N LYS 1 843 " --> pdb=" O GLU 1 839 " (cutoff:3.500A) Processing helix chain '1' and resid 845 through 854 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) Processing helix chain '1' and resid 855 through 859 removed outlier: 3.557A pdb=" N LYS 1 858 " --> pdb=" O ASP 1 855 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP 1 859 " --> pdb=" O ASP 1 856 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 855 through 859' Processing helix chain '1' and resid 861 through 880 Processing helix chain '1' and resid 885 through 901 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 908 through 922 Processing helix chain '1' and resid 923 through 927 removed outlier: 3.586A pdb=" N LYS 1 926 " --> pdb=" O LYS 1 923 " (cutoff:3.500A) Proline residue: 1 927 - end of helix No H-bonds generated for 'chain '1' and resid 923 through 927' Processing helix chain '1' and resid 928 through 940 Processing helix chain '1' and resid 944 through 958 Processing helix chain '1' and resid 958 through 965 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 967 through 981 removed outlier: 3.605A pdb=" N MET 1 971 " --> pdb=" O GLU 1 967 " (cutoff:3.500A) 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) Processing helix chain '1' and resid 982 through 984 No H-bonds generated for 'chain '1' and resid 982 through 984' Processing helix chain '1' and resid 986 through 1005 Processing helix chain '1' and resid 1012 through 1021 Proline residue: 11018 - end of helix Processing helix chain '1' and resid 1022 through 1026 Processing helix chain '1' and resid 1028 through 1046 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 1050 removed outlier: 3.787A pdb=" N VAL 11050 " --> pdb=" O ALA 11047 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1047 through 1050' Processing helix chain '1' and resid 1051 through 1062 Processing helix chain '1' and resid 1063 through 1068 removed outlier: 3.754A pdb=" N LEU 11066 " --> pdb=" O LEU 11063 " (cutoff:3.500A) Processing helix chain '1' and resid 1070 through 1089 removed outlier: 3.732A pdb=" N ARG 11074 " --> pdb=" O LYS 11070 " (cutoff:3.500A) 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 1089 through 1100 removed outlier: 3.715A pdb=" N VAL 11093 " --> pdb=" O GLY 11089 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR 11096 " --> pdb=" O ASP 11092 " (cutoff:3.500A) Processing helix chain '1' and resid 1101 through 1103 No H-bonds generated for 'chain '1' and resid 1101 through 1103' Processing helix chain '1' and resid 1105 through 1123 removed outlier: 3.504A pdb=" N ARG 11109 " --> pdb=" O GLU 11105 " (cutoff:3.500A) Processing helix chain '1' and resid 1124 through 1135 removed outlier: 4.204A pdb=" N VAL 11128 " --> pdb=" O SER 11124 " (cutoff:3.500A) Proline residue: 11130 - end of helix Processing helix chain '1' and resid 1136 through 1138 No H-bonds generated for 'chain '1' and resid 1136 through 1138' Processing helix chain '1' and resid 1140 through 1159 Processing helix chain '1' and resid 1160 through 1164 removed outlier: 3.539A pdb=" N ASP 11164 " --> pdb=" O MET 11161 " (cutoff:3.500A) Processing helix chain '1' and resid 1165 through 1178 Proline residue: 11171 - end of helix Processing helix chain '1' and resid 1181 through 1199 removed outlier: 3.508A pdb=" N ARG 11185 " --> pdb=" O ASP 11181 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY 11198 " --> pdb=" O HIS 11194 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL 11199 " --> pdb=" O MET 11195 " (cutoff:3.500A) Processing helix chain '1' and resid 1204 through 1216 removed outlier: 3.820A pdb=" N TYR 11214 " --> pdb=" O HIS 11210 " (cutoff:3.500A) Processing helix chain '1' and resid 1217 through 1221 removed outlier: 3.948A pdb=" N PHE 11220 " --> pdb=" O PRO 11217 " (cutoff:3.500A) Processing helix chain '1' and resid 1223 through 1242 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 1242 through 1251 removed outlier: 3.626A pdb=" N MET 11246 " --> pdb=" O GLY 11242 " (cutoff:3.500A) Processing helix chain '1' and resid 1252 through 1254 No H-bonds generated for 'chain '1' and resid 1252 through 1254' Processing helix chain '1' and resid 1258 through 1276 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 1278 through 1283 removed outlier: 3.642A pdb=" N ALA 11282 " --> pdb=" O ALA 11279 " (cutoff:3.500A) Processing helix chain '2' and resid 461 through 469 Processing helix chain '2' and resid 478 through 482 Processing helix chain '2' and resid 484 through 493 removed outlier: 3.556A pdb=" N ALA 2 493 " --> pdb=" O VAL 2 489 " (cutoff:3.500A) Processing helix chain '2' and resid 501 through 505 removed outlier: 3.983A pdb=" N CYS 2 505 " --> pdb=" O ARG 2 502 " (cutoff:3.500A) Processing helix chain '2' and resid 513 through 519 removed outlier: 3.808A pdb=" N LYS 2 519 " --> pdb=" O GLY 2 516 " (cutoff:3.500A) Processing helix chain '2' and resid 525 through 530 Processing helix chain '2' and resid 532 through 544 removed outlier: 3.606A pdb=" N MET 2 536 " --> pdb=" O GLY 2 532 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 555 Processing helix chain '2' and resid 567 through 577 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 613 No H-bonds generated for 'chain '2' and resid 612 through 613' Processing helix chain '2' and resid 615 through 617 No H-bonds generated for 'chain '2' and resid 615 through 617' Processing helix chain '2' and resid 632 through 640 removed outlier: 4.533A pdb=" N ARG 2 638 " --> pdb=" O ILE 2 634 " (cutoff:3.500A) Processing helix chain '2' and resid 691 through 703 removed outlier: 3.764A pdb=" N THR 2 696 " --> pdb=" O ALA 2 692 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 195 removed outlier: 3.788A pdb=" N ASP 3 195 " --> pdb=" O ALA 3 192 " (cutoff:3.500A) Processing helix chain '3' and resid 198 through 204 removed outlier: 3.587A pdb=" N ALA 3 202 " --> pdb=" O GLY 3 198 " (cutoff:3.500A) Processing helix chain '3' and resid 429 through 432 Processing helix chain '3' and resid 808 through 827 removed outlier: 3.572A pdb=" N VAL 3 824 " --> pdb=" O ALA 3 820 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA 3 827 " --> pdb=" O MET 3 823 " (cutoff:3.500A) Processing helix chain '3' and resid 834 through 845 removed outlier: 3.509A pdb=" N MET 3 838 " --> pdb=" O LEU 3 834 " (cutoff:3.500A) Processing helix chain '3' and resid 848 through 853 Processing helix chain '3' and resid 1134 through 1152 removed outlier: 3.951A pdb=" N SER 31150 " --> pdb=" O MET 31146 " (cutoff:3.500A) Processing helix chain '3' and resid 1159 through 1164 Processing helix chain '3' and resid 1176 through 1180 Processing helix chain '3' and resid 1181 through 1185 Processing helix chain '3' and resid 1186 through 1197 removed outlier: 4.086A pdb=" N GLU 31196 " --> pdb=" O ASN 31192 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU 31197 " --> pdb=" O VAL 31193 " (cutoff:3.500A) Processing helix chain '3' and resid 1200 through 1216 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 25 through 35 Processing helix chain '4' and resid 63 through 77 removed outlier: 4.210A pdb=" N ALA 4 67 " --> pdb=" O SER 4 63 " (cutoff:3.500A) 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 31 through 40 Processing helix chain '5' and resid 66 through 78 removed outlier: 3.701A pdb=" N SER 5 78 " --> pdb=" O CYS 5 74 " (cutoff:3.500A) Processing helix chain '5' and resid 102 through 118 Processing helix chain '6' and resid 46 through 55 removed outlier: 6.735A pdb=" N GLY 6 52 " --> pdb=" O CYS 6 49 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER 6 53 " --> pdb=" O ASN 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 73 through 78 Processing helix chain '6' and resid 79 through 83 removed outlier: 3.725A pdb=" N ARG 6 82 " --> pdb=" O GLU 6 79 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP 6 83 " --> pdb=" O LYS 6 80 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 79 through 83' Processing helix chain '6' and resid 91 through 106 removed outlier: 4.429A pdb=" N LYS 6 95 " --> pdb=" O LEU 6 91 " (cutoff:3.500A) 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 18 Processing helix chain '7' and resid 27 through 46 Processing helix chain '7' and resid 46 through 57 removed outlier: 3.528A pdb=" N LEU 7 50 " --> pdb=" O HIS 7 46 " (cutoff:3.500A) Processing helix chain '7' and resid 60 through 72 Processing helix chain 'h' and resid 5 through 13 Processing helix chain 'i' and resid 6 through 11 removed outlier: 4.261A pdb=" N LEU i 10 " --> pdb=" O SER i 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 9 removed outlier: 4.030A pdb=" N PHE j 6 " --> pdb=" O LYS j 2 " (cutoff:3.500A) Processing helix chain 'j' and resid 75 through 81 removed outlier: 3.654A pdb=" N VAL j 81 " --> pdb=" O ASP j 77 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 27 Processing helix chain 'k' and resid 29 through 39 Processing helix chain 'l' and resid 16 through 28 Processing helix chain 'm' and resid 6 through 15 Processing helix chain 'n' and resid 9 through 13 Processing helix chain 'v' and resid 9 through 27 Processing helix chain 'v' and resid 55 through 64 Processing helix chain 'v' and resid 65 through 74 removed outlier: 3.774A pdb=" N LEU v 74 " --> pdb=" O SER v 70 " (cutoff:3.500A) Processing helix chain 'v' and resid 184 through 199 Processing sheet with id=AA1, first strand: chain '1' and resid 412 through 414 Processing sheet with id=AA2, first strand: chain '3' and resid 1101 through 1108 removed outlier: 3.740A pdb=" N SER 31103 " --> pdb=" O THR 31120 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLU 31115 " --> pdb=" O PRO 31131 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE 31126 " --> pdb=" O LEU 3 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 16 through 20 removed outlier: 6.628A pdb=" N LEU 3 38 " --> pdb=" O THR 3 55 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR 3 55 " --> pdb=" O LEU 3 38 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU 3 40 " --> pdb=" O LEU 3 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 62 through 68 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: 6.292A pdb=" N ILE 3 87 " --> pdb=" O GLN 3 104 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN 3 104 " --> pdb=" O ILE 3 87 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE 3 89 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AA6, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AA7, first strand: chain '3' and resid 165 through 173 removed outlier: 5.462A pdb=" N VAL 3 167 " --> pdb=" O MET 3 187 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N MET 3 187 " --> pdb=" O VAL 3 167 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS 3 169 " --> pdb=" O LEU 3 185 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET 3 181 " --> pdb=" O VAL 3 173 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU 3 208 " --> pdb=" O SER 3 225 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER 3 225 " --> pdb=" O LEU 3 208 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE 3 210 " --> pdb=" O LYS 3 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 232 through 237 removed outlier: 7.103A pdb=" N CYS 3 251 " --> pdb=" O ASN 3 233 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU 3 235 " --> pdb=" O LEU 3 249 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU 3 249 " --> pdb=" O LEU 3 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 273 through 274 removed outlier: 6.444A pdb=" N ARG 3 273 " --> pdb=" O PHE 3 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '3' and resid 287 through 294 removed outlier: 3.839A pdb=" N CYS 3 289 " --> pdb=" O GLN 3 304 " (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: 6.703A pdb=" N ILE 3 310 " --> pdb=" O PHE 3 330 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU 3 324 " --> pdb=" O GLU 3 316 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASP 3 318 " --> pdb=" O VAL 3 322 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL 3 322 " --> pdb=" O ASP 3 318 " (cutoff:3.500A) Processing sheet with id=AB2, 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: 6.478A pdb=" N HIS 3 356 " --> pdb=" O GLU 3 400 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU 3 400 " --> pdb=" O HIS 3 356 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU 3 358 " --> pdb=" O VAL 3 398 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 407 through 413 removed outlier: 6.468A pdb=" N ALA 3 426 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N CYS 3 410 " --> pdb=" O TYR 3 424 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR 3 424 " --> pdb=" O CYS 3 410 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE 3 412 " --> pdb=" O GLN 3 422 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN 3 422 " --> pdb=" O ILE 3 412 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 445 through 450 removed outlier: 6.535A pdb=" N ILE 3 764 " --> pdb=" O MET 3 447 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL 3 449 " --> pdb=" O LEU 3 762 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU 3 762 " --> pdb=" O VAL 3 449 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 456 through 462 removed outlier: 3.546A pdb=" N ALA 3 458 " --> pdb=" O SER 3 477 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU 3 492 " --> pdb=" O SER 3 486 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '3' and resid 507 through 509 Processing sheet with id=AB7, first strand: chain '3' and resid 544 through 549 removed outlier: 6.678A pdb=" N ALA 3 557 " --> pdb=" O VAL 3 545 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS 3 547 " --> pdb=" O VAL 3 555 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL 3 555 " --> pdb=" O CYS 3 547 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL 3 549 " --> pdb=" O GLN 3 553 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN 3 553 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU 3 562 " --> pdb=" O LEU 3 558 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '3' and resid 587 through 592 removed outlier: 3.591A pdb=" N CYS 3 589 " --> pdb=" O GLY 3 608 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TPO 3 613 " --> pdb=" O LEU 3 609 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL 3 614 " --> pdb=" O SER 3 629 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER 3 629 " --> pdb=" O VAL 3 614 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE 3 616 " --> pdb=" O PRO 3 627 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SER 3 618 " --> pdb=" O LEU 3 625 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '3' and resid 637 through 645 removed outlier: 3.665A pdb=" N SER 3 639 " --> pdb=" O GLY 3 668 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET 3 645 " --> pdb=" O PHE 3 662 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU 3 669 " --> pdb=" O VAL 3 673 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL 3 673 " --> pdb=" O LEU 3 669 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG 3 676 " --> pdb=" O ARG 3 690 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '3' and resid 700 through 703 Processing sheet with id=AC2, 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: 7.668A pdb=" N SER 3 864 " --> pdb=" O GLN 3 881 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLN 3 881 " --> pdb=" O SER 3 864 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE 3 866 " --> pdb=" O LEU 3 879 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU 3 879 " --> pdb=" O ILE 3 866 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL 3 868 " --> pdb=" O LEU 3 877 " (cutoff:3.500A) Processing sheet with id=AC3, 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=AC4, first strand: chain '3' and resid 949 through 955 removed outlier: 3.869A pdb=" N ALA 3 951 " --> pdb=" O GLY 3 962 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL 3 969 " --> pdb=" O CYS 3 981 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N CYS 3 981 " --> pdb=" O VAL 3 969 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP 3 971 " --> pdb=" O ARG 3 979 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG 3 979 " --> pdb=" O ASP 3 971 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 990 through 996 removed outlier: 3.616A pdb=" N GLY 3 992 " --> pdb=" O SER 31003 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE 31009 " --> pdb=" O ASP 31026 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASP 31026 " --> pdb=" O PHE 31009 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP 31011 " --> pdb=" O PHE 31024 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN 31087 " --> pdb=" O PHE 31024 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 1033 through 1038 removed outlier: 3.848A pdb=" N THR 31035 " --> pdb=" O ALA 31047 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN 31052 " --> pdb=" O ASP 31048 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE 31053 " --> pdb=" O ASN 31094 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN 31094 " --> pdb=" O ILE 31053 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL 31055 " --> pdb=" O ILE 31092 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '4' and resid 41 through 43 Processing sheet with id=AC8, first strand: chain '5' and resid 81 through 82 Processing sheet with id=AC9, first strand: chain '6' and resid 18 through 19 removed outlier: 3.894A pdb=" N ALA 6 18 " --> pdb=" O ILE 6 45 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '6' and resid 21 through 22 Processing sheet with id=AD2, first strand: chain '6' and resid 39 through 42 Processing sheet with id=AD3, first strand: chain 'h' and resid 17 through 22 removed outlier: 6.817A pdb=" N TYR h 28 " --> pdb=" O VAL h 48 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL h 48 " --> pdb=" O TYR h 28 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY h 30 " --> pdb=" O ILE h 46 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE h 46 " --> pdb=" O GLY h 30 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU h 32 " --> pdb=" O SER h 44 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER h 44 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU h 59 " --> pdb=" O ASN h 45 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR h 47 " --> pdb=" O GLN h 57 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLN h 57 " --> pdb=" O THR h 47 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR h 49 " --> pdb=" O VAL h 55 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL h 55 " --> pdb=" O THR h 49 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN h 60 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N HIS n 26 " --> pdb=" O GLU n 47 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU n 47 " --> pdb=" O HIS n 26 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN n 28 " --> pdb=" O CYS n 45 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS n 45 " --> pdb=" O GLN n 28 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU n 44 " --> pdb=" O GLY n 58 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLY n 58 " --> pdb=" O GLU n 44 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL n 46 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN n 56 " --> pdb=" O VAL n 46 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N MET n 59 " --> pdb=" O SER l 89 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N SER l 89 " --> pdb=" O MET n 59 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP l 34 " --> pdb=" O THR l 85 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU l 87 " --> pdb=" O GLN l 32 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN l 32 " --> pdb=" O LEU l 87 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER l 89 " --> pdb=" O ARG l 30 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG l 30 " --> pdb=" O SER l 89 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N CYS l 46 " --> pdb=" O ASP l 60 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP l 60 " --> pdb=" O CYS l 46 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE l 48 " --> pdb=" O LEU l 58 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU l 58 " --> pdb=" O ILE l 48 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE l 50 " --> pdb=" O LEU l 56 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU l 56 " --> pdb=" O PHE l 50 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL l 57 " --> pdb=" O MET l 78 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET l 78 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP l 59 " --> pdb=" O ARG l 76 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG l 76 " --> pdb=" O ASP l 59 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ARG l 76 " --> pdb=" O GLY m 74 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY m 74 " --> pdb=" O ARG l 76 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR m 32 " --> pdb=" O ASN m 46 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASN m 46 " --> pdb=" O TYR m 32 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL m 34 " --> pdb=" O LEU m 44 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU m 44 " --> pdb=" O VAL m 34 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL m 36 " --> pdb=" O MET m 42 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N MET m 42 " --> pdb=" O VAL m 36 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN m 43 " --> pdb=" O VAL m 62 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL m 62 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA m 45 " --> pdb=" O GLY m 60 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY m 60 " --> pdb=" O ALA m 45 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR m 47 " --> pdb=" O HIS m 58 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS m 58 " --> pdb=" O THR m 47 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU m 49 " --> pdb=" O SER m 56 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU m 61 " --> pdb=" O ARG k 111 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ARG k 55 " --> pdb=" O ASN k 69 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASN k 69 " --> pdb=" O ARG k 55 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS k 57 " --> pdb=" O LEU k 67 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU k 67 " --> pdb=" O LYS k 57 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE k 59 " --> pdb=" O MET k 65 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET k 65 " --> pdb=" O PHE k 59 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER k 97 " --> pdb=" O ASN k 69 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS k 71 " --> pdb=" O TYR k 95 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR k 95 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET k 73 " --> pdb=" O ASP k 93 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP k 93 " --> pdb=" O MET k 73 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR k 75 " --> pdb=" O ASN k 91 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN k 91 " --> pdb=" O THR k 75 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR j 28 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA j 42 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR j 30 " --> pdb=" O LEU j 40 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU j 40 " --> pdb=" O THR j 30 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL j 32 " --> pdb=" O THR j 38 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR j 38 " --> pdb=" O VAL j 32 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU j 56 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS j 44 " --> pdb=" O GLN j 54 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN j 54 " --> pdb=" O LYS j 44 " (cutoff:3.500A) removed outlier: 14.289A pdb=" N LEU j 55 " --> pdb=" O GLY i 84 " (cutoff:3.500A) removed outlier: 12.665A pdb=" N GLY i 84 " --> pdb=" O LEU j 55 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR j 57 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL i 82 " --> pdb=" O THR j 57 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG i 16 " --> pdb=" O GLU i 83 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE i 26 " --> pdb=" O GLU i 47 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU i 47 " --> pdb=" O ILE i 26 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE i 28 " --> pdb=" O CYS i 45 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS i 45 " --> pdb=" O ILE i 28 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE i 41 " --> pdb=" O LYS i 32 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLY i 68 " --> pdb=" O ASP i 44 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP i 46 " --> pdb=" O VAL i 66 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL i 66 " --> pdb=" O ASP i 46 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE i 48 " --> pdb=" O LYS i 64 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS i 64 " --> pdb=" O PHE i 48 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU i 69 " --> pdb=" O LEU h 73 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'v' and resid 34 through 36 1191 hydrogen bonds defined for protein. 3306 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: 12.51 Time building geometry restraints manager: 12.08 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: 509 2.64 - 3.20: 23827 3.20 - 3.77: 41433 3.77 - 4.33: 54716 4.33 - 4.90: 92084 Nonbonded interactions: 212569 Sorted by model distance: nonbonded pdb=" O2' C A 206 " pdb=" OP2 A A 207 " model vdw 2.073 3.040 nonbonded pdb=" O SER 11276 " pdb=" OG SER 11276 " model vdw 2.191 3.040 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 3.040 nonbonded pdb=" NH2 ARG v 5 " pdb=" O GLY v 7 " model vdw 2.253 3.120 ... (remaining 212564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 7.930 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: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 88.120 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.140 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.280 ------------------------------------------------------------------------------- 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= 1.529 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 : 2.897 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: 0.4035 time to fit residues: 153.4080 Evaluate side-chains 148 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 3.018 ------------------------------------------------------------------------------- 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: 10.0000 chunk 259 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 268 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 200 optimal weight: 40.0000 chunk 311 optimal weight: 40.0000 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 ** 1 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 912 ASN 11184 HIS ** 11209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 579 GLN ** 2 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 51 HIS ** 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 31020 GLN 6 78 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1072 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27582 Z= 0.191 Angle : 0.610 9.871 37808 Z= 0.327 Chirality : 0.044 0.197 4393 Planarity : 0.005 0.054 4668 Dihedral : 13.037 153.330 4890 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.26 (0.14), residues: 3364 helix: 0.17 (0.15), residues: 1080 sheet: 0.01 (0.19), residues: 687 loop : -0.36 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 2 578 HIS 0.005 0.001 HIS 31135 PHE 0.017 0.002 PHE 31217 TYR 0.027 0.002 TYR 1 412 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 136 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1162 (tpp) cc_final: 0.0566 (ttt) REVERT: 1 511 MET cc_start: 0.4228 (mmp) cc_final: 0.3678 (mmt) REVERT: 1 609 MET cc_start: -0.1284 (mmt) cc_final: -0.2441 (tmm) REVERT: 1 656 LYS cc_start: 0.2878 (mmpt) cc_final: 0.1392 (pttt) REVERT: 1 675 MET cc_start: -0.0107 (mtp) cc_final: -0.0479 (mmt) REVERT: 1 867 MET cc_start: 0.3149 (tpt) cc_final: 0.2601 (tpt) REVERT: 1 1178 MET cc_start: 0.5352 (ptm) cc_final: 0.4785 (ptm) REVERT: 3 339 MET cc_start: 0.1534 (mtm) cc_final: 0.1206 (mmm) REVERT: 3 583 MET cc_start: -0.3147 (mtm) cc_final: -0.3352 (mtt) REVERT: 3 1146 MET cc_start: -0.0115 (mtm) cc_final: -0.0754 (ttp) REVERT: 3 1185 MET cc_start: -0.1515 (mtm) cc_final: -0.2281 (tpt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3498 time to fit residues: 82.7750 Evaluate side-chains 127 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.852 ------------------------------------------------------------------------------- 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: 6.9990 chunk 96 optimal weight: 30.0000 chunk 259 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 312 optimal weight: 40.0000 chunk 337 optimal weight: 9.9990 chunk 277 optimal weight: 60.0000 chunk 309 optimal weight: 40.0000 chunk 106 optimal weight: 0.0370 chunk 250 optimal weight: 0.9980 overall best weight: 9.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 547 GLN 1 804 ASN 1 817 HIS 1 901 GLN 2 496 ASN 2 695 GLN ** 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** 6 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1131 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27582 Z= 0.165 Angle : 0.539 9.307 37808 Z= 0.287 Chirality : 0.042 0.412 4393 Planarity : 0.004 0.052 4668 Dihedral : 12.790 162.112 4890 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.08 % Allowed : 2.38 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.19 (0.14), residues: 3364 helix: 0.75 (0.15), residues: 1095 sheet: -0.03 (0.19), residues: 733 loop : -0.10 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 632 HIS 0.005 0.001 HIS 3 169 PHE 0.033 0.001 PHE 11155 TYR 0.020 0.001 TYR 1 805 ARG 0.012 0.000 ARG 3 615 *********************** 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 134 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1193 (tpp) cc_final: 0.0036 (ttt) REVERT: 1 156 MET cc_start: -0.1947 (mmm) cc_final: -0.2633 (ptp) REVERT: 1 511 MET cc_start: 0.3946 (mmp) cc_final: 0.3484 (mmt) REVERT: 1 609 MET cc_start: -0.1837 (mmt) cc_final: -0.2539 (tmm) REVERT: 1 656 LYS cc_start: 0.2826 (mmpt) cc_final: 0.1097 (pttt) REVERT: 1 675 MET cc_start: -0.0087 (mtp) cc_final: -0.0352 (mmt) REVERT: 1 867 MET cc_start: 0.4206 (tpt) cc_final: 0.3580 (tpt) REVERT: 1 876 MET cc_start: 0.3670 (mtt) cc_final: 0.3379 (mtt) REVERT: 1 1178 MET cc_start: 0.5239 (ptm) cc_final: 0.4698 (ptm) REVERT: 3 339 MET cc_start: 0.1648 (mtm) cc_final: 0.1428 (mmm) REVERT: 3 447 MET cc_start: 0.0327 (mmm) cc_final: -0.0929 (mtt) REVERT: 3 1146 MET cc_start: -0.0571 (mtm) cc_final: -0.0839 (ttp) REVERT: 3 1185 MET cc_start: -0.1133 (mtm) cc_final: -0.2180 (tpt) REVERT: 5 26 LEU cc_start: 0.5226 (mm) cc_final: 0.4832 (mt) outliers start: 2 outliers final: 0 residues processed: 134 average time/residue: 0.3489 time to fit residues: 79.6564 Evaluate side-chains 124 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.953 ------------------------------------------------------------------------------- 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: 50.0000 chunk 161 optimal weight: 50.0000 chunk 34 optimal weight: 8.9990 chunk 148 optimal weight: 40.0000 chunk 209 optimal weight: 0.0470 chunk 313 optimal weight: 7.9990 chunk 331 optimal weight: 50.0000 chunk 163 optimal weight: 40.0000 chunk 296 optimal weight: 9.9990 chunk 89 optimal weight: 50.0000 overall best weight: 13.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11034 ASN ** 11256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 572 HIS ** 3 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 796 ASN ** 6 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1241 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27582 Z= 0.186 Angle : 0.581 11.830 37808 Z= 0.307 Chirality : 0.043 0.216 4393 Planarity : 0.005 0.054 4668 Dihedral : 12.877 159.885 4890 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.04 % Allowed : 2.42 % Favored : 97.54 % 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: 0.20 (0.14), residues: 3364 helix: 0.84 (0.16), residues: 1089 sheet: -0.11 (0.19), residues: 741 loop : -0.12 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 31011 HIS 0.007 0.001 HIS 31138 PHE 0.021 0.002 PHE 11155 TYR 0.027 0.002 TYR 1 830 ARG 0.008 0.001 ARG 5 49 *********************** 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 136 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1238 (tpp) cc_final: -0.0005 (ttt) REVERT: 1 511 MET cc_start: 0.3842 (mmp) cc_final: 0.3266 (mmp) REVERT: 1 609 MET cc_start: -0.1319 (mmt) cc_final: -0.2198 (tmm) REVERT: 1 620 MET cc_start: 0.3842 (tmm) cc_final: 0.2633 (ttm) REVERT: 1 656 LYS cc_start: 0.2658 (mmpt) cc_final: 0.0609 (pttt) REVERT: 1 867 MET cc_start: 0.4276 (tpt) cc_final: 0.3458 (tpt) REVERT: 1 876 MET cc_start: 0.3187 (mtt) cc_final: 0.2987 (mtt) REVERT: 1 1178 MET cc_start: 0.4917 (ptm) cc_final: 0.4265 (ptm) REVERT: 2 653 LEU cc_start: 0.2536 (tp) cc_final: 0.2331 (tt) REVERT: 3 66 MET cc_start: 0.2596 (tpt) cc_final: 0.2232 (mmp) REVERT: 3 339 MET cc_start: 0.2190 (mtm) cc_final: 0.1599 (mmm) REVERT: 3 869 MET cc_start: -0.0408 (ppp) cc_final: -0.2367 (mtm) REVERT: 3 1185 MET cc_start: -0.0466 (mtm) cc_final: -0.1601 (tpt) REVERT: 5 92 TYR cc_start: 0.1831 (t80) cc_final: 0.1296 (t80) REVERT: 7 72 MET cc_start: -0.0438 (ptp) cc_final: -0.0873 (ptp) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.3408 time to fit residues: 80.1764 Evaluate side-chains 124 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.858 ------------------------------------------------------------------------------- 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: 10.0000 chunk 246 optimal weight: 50.0000 chunk 136 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 169 optimal weight: 50.0000 chunk 297 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- 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** 1 737 GLN 1 804 ASN 11108 ASN ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 78 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: 0.1236 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27582 Z= 0.145 Angle : 0.504 9.495 37808 Z= 0.268 Chirality : 0.042 0.229 4393 Planarity : 0.004 0.056 4668 Dihedral : 12.872 162.679 4890 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: 0.34 (0.15), residues: 3364 helix: 1.02 (0.16), residues: 1096 sheet: -0.07 (0.19), residues: 727 loop : -0.07 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 819 HIS 0.005 0.001 HIS 11194 PHE 0.016 0.001 PHE 11155 TYR 0.020 0.001 TYR 5 61 ARG 0.004 0.000 ARG 3 763 *********************** 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 126 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 126 MET cc_start: -0.3486 (mtm) cc_final: -0.3729 (mtm) REVERT: 1 147 MET cc_start: 0.1267 (tpp) cc_final: -0.0142 (ttt) REVERT: 1 156 MET cc_start: -0.2423 (mmt) cc_final: -0.3525 (ptm) REVERT: 1 446 MET cc_start: 0.2932 (mpp) cc_final: -0.1227 (ppp) REVERT: 1 511 MET cc_start: 0.4088 (mmp) cc_final: 0.3494 (mmp) REVERT: 1 609 MET cc_start: -0.1985 (mmt) cc_final: -0.2342 (tmm) REVERT: 1 656 LYS cc_start: 0.2660 (mmpt) cc_final: 0.0372 (pttt) REVERT: 1 867 MET cc_start: 0.4464 (tpt) cc_final: 0.3787 (tpt) REVERT: 1 876 MET cc_start: 0.3268 (mtt) cc_final: 0.2975 (mtt) REVERT: 1 1178 MET cc_start: 0.5043 (ptm) cc_final: 0.4490 (ptm) REVERT: 3 339 MET cc_start: 0.2574 (mtm) cc_final: 0.1963 (mmm) REVERT: 3 447 MET cc_start: 0.0846 (mmm) cc_final: -0.0599 (mtt) REVERT: 3 1185 MET cc_start: -0.0460 (mtm) cc_final: -0.1140 (tpt) REVERT: 5 26 LEU cc_start: 0.4947 (mm) cc_final: 0.4584 (mt) REVERT: 7 69 MET cc_start: -0.0735 (mpp) cc_final: -0.1091 (ptp) REVERT: 7 72 MET cc_start: -0.0625 (ptp) cc_final: -0.1014 (ptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3583 time to fit residues: 78.5232 Evaluate side-chains 122 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 3.026 ------------------------------------------------------------------------------- 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: 9.9990 chunk 65 optimal weight: 6.9990 chunk 194 optimal weight: 50.0000 chunk 81 optimal weight: 9.9990 chunk 331 optimal weight: 50.0000 chunk 275 optimal weight: 70.0000 chunk 153 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 109 optimal weight: 0.4980 chunk 174 optimal weight: 7.9990 overall best weight: 7.0988 ------------------------------------------------------------------------------- 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** 1 817 HIS ** 1 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 709 GLN ** 5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 78 GLN ** 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: 0.1246 moved from start: 0.5326 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= 0.132 Angle : 0.493 9.544 37808 Z= 0.260 Chirality : 0.041 0.223 4393 Planarity : 0.004 0.058 4668 Dihedral : 12.804 159.579 4890 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: 0.49 (0.15), residues: 3364 helix: 1.24 (0.16), residues: 1099 sheet: -0.07 (0.19), residues: 740 loop : -0.02 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 3 720 HIS 0.003 0.001 HIS 3 231 PHE 0.023 0.001 PHE 11155 TYR 0.019 0.001 TYR 1 830 ARG 0.003 0.000 ARG 3 615 *********************** 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: 0 poor density : 129 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 126 MET cc_start: -0.3395 (mtm) cc_final: -0.3646 (mtm) REVERT: 1 147 MET cc_start: 0.0948 (tpp) cc_final: -0.0365 (ttt) REVERT: 1 446 MET cc_start: 0.3097 (mpp) cc_final: -0.1172 (ppp) REVERT: 1 511 MET cc_start: 0.3720 (mmp) cc_final: 0.3142 (mmp) REVERT: 1 620 MET cc_start: 0.4006 (tmm) cc_final: 0.2755 (mtm) REVERT: 1 656 LYS cc_start: 0.2183 (mmpt) cc_final: -0.0064 (pttp) REVERT: 1 867 MET cc_start: 0.4361 (tpt) cc_final: 0.3597 (tpt) REVERT: 1 869 MET cc_start: 0.0099 (tmm) cc_final: -0.0342 (tmm) REVERT: 1 876 MET cc_start: 0.3463 (mtt) cc_final: 0.3020 (mtt) REVERT: 1 1178 MET cc_start: 0.5143 (ptm) cc_final: 0.4558 (ptm) REVERT: 3 339 MET cc_start: 0.2979 (mtm) cc_final: 0.2261 (mmm) REVERT: 3 447 MET cc_start: 0.0831 (mmm) cc_final: -0.0612 (mtt) REVERT: 3 583 MET cc_start: -0.3879 (mtt) cc_final: -0.5242 (mmt) REVERT: 3 1185 MET cc_start: -0.0545 (mtm) cc_final: -0.0942 (tpt) REVERT: 5 26 LEU cc_start: 0.4856 (mm) cc_final: 0.4470 (mt) REVERT: 5 92 TYR cc_start: 0.2141 (t80) cc_final: 0.1687 (t80) REVERT: 7 72 MET cc_start: -0.0829 (ptp) cc_final: -0.1590 (ptt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3525 time to fit residues: 78.8188 Evaluate side-chains 121 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.833 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 50.0000 chunk 189 optimal weight: 3.9990 chunk 242 optimal weight: 50.0000 chunk 187 optimal weight: 30.0000 chunk 279 optimal weight: 50.0000 chunk 185 optimal weight: 50.0000 chunk 330 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 201 optimal weight: 40.0000 chunk 152 optimal weight: 40.0000 overall best weight: 12.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 698 GLN ** 1 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 829 ASN ** 11256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 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: 0.1310 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 27582 Z= 0.170 Angle : 0.543 10.856 37808 Z= 0.284 Chirality : 0.042 0.231 4393 Planarity : 0.004 0.057 4668 Dihedral : 12.956 163.500 4890 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.04 % Allowed : 1.25 % Favored : 98.71 % 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 (0.15), residues: 3364 helix: 1.11 (0.16), residues: 1093 sheet: -0.05 (0.20), residues: 708 loop : -0.03 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 31011 HIS 0.005 0.001 HIS 11184 PHE 0.018 0.001 PHE 2 527 TYR 0.020 0.002 TYR 1 830 ARG 0.006 0.001 ARG 3 763 *********************** 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 128 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1153 (tpp) cc_final: -0.0467 (ttt) REVERT: 1 156 MET cc_start: -0.2605 (tpp) cc_final: -0.3859 (ptm) REVERT: 1 446 MET cc_start: 0.2928 (mpp) cc_final: -0.1279 (ppp) REVERT: 1 511 MET cc_start: 0.3473 (mmp) cc_final: 0.2978 (mmp) REVERT: 1 867 MET cc_start: 0.4653 (tpt) cc_final: 0.3791 (tpt) REVERT: 1 869 MET cc_start: 0.0278 (tmm) cc_final: -0.0666 (tmm) REVERT: 1 1178 MET cc_start: 0.5043 (ptm) cc_final: 0.4629 (ptm) REVERT: 2 526 ASP cc_start: 0.6928 (p0) cc_final: 0.6720 (p0) REVERT: 3 339 MET cc_start: 0.3285 (mtm) cc_final: 0.2557 (mmm) REVERT: 3 447 MET cc_start: 0.1299 (mmm) cc_final: -0.0079 (mmm) REVERT: 3 583 MET cc_start: -0.3297 (mtt) cc_final: -0.3954 (tpp) REVERT: 3 1185 MET cc_start: -0.0306 (mtm) cc_final: -0.0852 (tpt) REVERT: 5 92 TYR cc_start: 0.2179 (t80) cc_final: 0.1682 (t80) REVERT: 7 69 MET cc_start: -0.0470 (mpp) cc_final: -0.0860 (ptp) REVERT: 7 72 MET cc_start: -0.0734 (ptp) cc_final: -0.1256 (ptt) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.3287 time to fit residues: 74.2077 Evaluate side-chains 119 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.879 ------------------------------------------------------------------------------- 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: 2.9990 chunk 132 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 99 optimal weight: 50.0000 chunk 64 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 chunk 163 optimal weight: 30.0000 chunk 30 optimal weight: 50.0000 chunk 259 optimal weight: 40.0000 chunk 300 optimal weight: 20.0000 overall best weight: 5.3790 ------------------------------------------------------------------------------- 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** 3 103 HIS ** 3 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 52 ASN ** 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: 0.1280 moved from start: 0.6310 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= 0.124 Angle : 0.491 10.628 37808 Z= 0.256 Chirality : 0.041 0.222 4393 Planarity : 0.004 0.061 4668 Dihedral : 12.893 160.051 4890 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.55 (0.15), residues: 3364 helix: 1.33 (0.16), residues: 1098 sheet: -0.06 (0.19), residues: 719 loop : 0.01 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 578 HIS 0.004 0.001 HIS 3 293 PHE 0.017 0.001 PHE 11153 TYR 0.023 0.001 TYR 5 61 ARG 0.007 0.000 ARG 5 49 *********************** 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 126 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 3.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1073 (tpp) cc_final: -0.0515 (ttt) REVERT: 1 156 MET cc_start: -0.2624 (tpp) cc_final: -0.3715 (ptm) REVERT: 1 446 MET cc_start: 0.3199 (mpp) cc_final: -0.0816 (ppp) REVERT: 1 511 MET cc_start: 0.3120 (mmp) cc_final: 0.2675 (mmp) REVERT: 1 620 MET cc_start: 0.4201 (tmm) cc_final: 0.3114 (mtt) REVERT: 1 675 MET cc_start: 0.0039 (tpt) cc_final: -0.0483 (tpt) REVERT: 1 867 MET cc_start: 0.4587 (tpt) cc_final: 0.3675 (tpt) REVERT: 1 869 MET cc_start: 0.0312 (tmm) cc_final: -0.0524 (tmm) REVERT: 1 1178 MET cc_start: 0.5127 (ptm) cc_final: 0.4544 (ptm) REVERT: 2 526 ASP cc_start: 0.6829 (p0) cc_final: 0.6603 (p0) REVERT: 3 339 MET cc_start: 0.3002 (mtm) cc_final: 0.2581 (mmm) REVERT: 3 447 MET cc_start: 0.1353 (mmm) cc_final: -0.0049 (mmm) REVERT: 3 583 MET cc_start: -0.2973 (mtt) cc_final: -0.4298 (tpp) REVERT: 3 1185 MET cc_start: -0.0086 (mtm) cc_final: -0.0539 (tpt) REVERT: 7 69 MET cc_start: -0.0177 (mpp) cc_final: -0.0556 (ptp) REVERT: 7 72 MET cc_start: -0.0751 (ptp) cc_final: -0.1309 (ptt) REVERT: v 36 MET cc_start: -0.0263 (mmt) cc_final: -0.0569 (mmp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3463 time to fit residues: 76.4838 Evaluate side-chains 119 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.849 ------------------------------------------------------------------------------- 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: 20.0000 chunk 288 optimal weight: 5.9990 chunk 308 optimal weight: 40.0000 chunk 185 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 241 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 278 optimal weight: 60.0000 chunk 291 optimal weight: 50.0000 chunk 306 optimal weight: 10.0000 chunk 202 optimal weight: 0.0030 overall best weight: 6.4000 ------------------------------------------------------------------------------- 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** ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 859 ASN ** 5 52 ASN ** 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: 0.1290 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27582 Z= 0.127 Angle : 0.484 9.609 37808 Z= 0.254 Chirality : 0.041 0.222 4393 Planarity : 0.004 0.058 4668 Dihedral : 12.876 160.987 4890 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 0.60 (0.15), residues: 3364 helix: 1.37 (0.16), residues: 1105 sheet: -0.01 (0.20), residues: 715 loop : 0.02 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 658 HIS 0.003 0.001 HIS 3 169 PHE 0.010 0.001 PHE 2 527 TYR 0.023 0.001 TYR 3 577 ARG 0.003 0.000 ARG 3 763 *********************** 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 126 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1196 (tpp) cc_final: -0.0407 (ttt) REVERT: 1 156 MET cc_start: -0.2501 (tpp) cc_final: -0.3721 (ptp) REVERT: 1 446 MET cc_start: 0.3038 (mpp) cc_final: -0.0720 (ppp) REVERT: 1 620 MET cc_start: 0.4434 (tmm) cc_final: 0.3324 (mtt) REVERT: 1 656 LYS cc_start: 0.2213 (mmpt) cc_final: -0.0646 (pttp) REVERT: 1 675 MET cc_start: 0.0097 (tpt) cc_final: -0.0421 (tpt) REVERT: 1 867 MET cc_start: 0.4310 (tpt) cc_final: 0.3322 (tpt) REVERT: 1 869 MET cc_start: 0.0280 (tmm) cc_final: -0.0009 (tmm) REVERT: 1 1178 MET cc_start: 0.4555 (ptm) cc_final: 0.3996 (ptm) REVERT: 2 526 ASP cc_start: 0.6637 (p0) cc_final: 0.6355 (p0) REVERT: 2 653 LEU cc_start: 0.2426 (tt) cc_final: 0.1742 (pt) REVERT: 3 66 MET cc_start: 0.1655 (tpt) cc_final: 0.1054 (tpp) REVERT: 3 339 MET cc_start: 0.2946 (mtm) cc_final: 0.2491 (mmm) REVERT: 3 447 MET cc_start: 0.1388 (mmm) cc_final: 0.0024 (mmm) REVERT: 3 583 MET cc_start: -0.2939 (mtt) cc_final: -0.4212 (tpp) REVERT: 3 1185 MET cc_start: -0.0161 (mtm) cc_final: -0.0541 (tpt) REVERT: 7 69 MET cc_start: -0.0128 (mpp) cc_final: -0.0579 (ptp) REVERT: 7 72 MET cc_start: -0.0970 (ptp) cc_final: -0.1334 (ptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3398 time to fit residues: 75.7068 Evaluate side-chains 118 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.113 ------------------------------------------------------------------------------- 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: 30.0000 chunk 198 optimal weight: 30.0000 chunk 154 optimal weight: 9.9990 chunk 226 optimal weight: 0.0570 chunk 341 optimal weight: 50.0000 chunk 314 optimal weight: 9.9990 chunk 272 optimal weight: 30.0000 chunk 28 optimal weight: 4.9990 chunk 210 optimal weight: 50.0000 chunk 166 optimal weight: 10.0000 chunk 216 optimal weight: 40.0000 overall best weight: 7.0108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11225 HIS ** 11256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 103 HIS ** 3 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 219 HIS ** 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: 0.6868 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= 0.129 Angle : 0.488 9.612 37808 Z= 0.254 Chirality : 0.041 0.216 4393 Planarity : 0.004 0.057 4668 Dihedral : 12.881 160.398 4890 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 0.66 (0.15), residues: 3364 helix: 1.39 (0.16), residues: 1102 sheet: -0.05 (0.20), residues: 723 loop : 0.11 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 658 HIS 0.006 0.001 HIS 3 219 PHE 0.011 0.001 PHE 11153 TYR 0.017 0.001 TYR 3 577 ARG 0.003 0.000 ARG 3 326 ********************** 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 128 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 147 MET cc_start: 0.1096 (tpp) cc_final: -0.0593 (ttt) REVERT: 1 446 MET cc_start: 0.3039 (mpp) cc_final: -0.0739 (ppp) REVERT: 1 620 MET cc_start: 0.4634 (tmm) cc_final: 0.3636 (mtt) REVERT: 1 656 LYS cc_start: 0.2196 (mmpt) cc_final: -0.0623 (pttp) REVERT: 1 675 MET cc_start: 0.0299 (tpt) cc_final: -0.0252 (tpt) REVERT: 1 867 MET cc_start: 0.3906 (tpt) cc_final: 0.3067 (tpt) REVERT: 1 869 MET cc_start: 0.0342 (tmm) cc_final: 0.0000 (tmm) REVERT: 1 1178 MET cc_start: 0.4477 (ptm) cc_final: 0.3980 (ptm) REVERT: 1 1231 MET cc_start: 0.0781 (ppp) cc_final: 0.0404 (ppp) REVERT: 2 526 ASP cc_start: 0.6633 (p0) cc_final: 0.6362 (p0) REVERT: 2 653 LEU cc_start: 0.2491 (tt) cc_final: 0.1746 (pt) REVERT: 3 66 MET cc_start: 0.1652 (tpt) cc_final: 0.1017 (tpp) REVERT: 3 131 MET cc_start: 0.0629 (ppp) cc_final: 0.0395 (ppp) REVERT: 3 339 MET cc_start: 0.3140 (mtm) cc_final: 0.2477 (mmm) REVERT: 3 447 MET cc_start: 0.1308 (mmm) cc_final: 0.0043 (mmm) REVERT: 3 583 MET cc_start: -0.2769 (mtt) cc_final: -0.4106 (tpp) REVERT: 3 838 MET cc_start: -0.3922 (tpt) cc_final: -0.5830 (tmm) REVERT: 3 1185 MET cc_start: 0.0022 (mtm) cc_final: -0.0363 (tpt) REVERT: 7 72 MET cc_start: -0.0997 (ptp) cc_final: -0.1735 (ptt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3513 time to fit residues: 77.9992 Evaluate side-chains 119 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.3916 > 50: distance: 16 - 23: 15.019 distance: 17 - 48: 32.212 distance: 23 - 24: 12.827 distance: 24 - 25: 43.044 distance: 24 - 27: 26.630 distance: 25 - 26: 24.107 distance: 25 - 28: 25.219 distance: 26 - 56: 48.452 distance: 28 - 29: 16.125 distance: 29 - 30: 15.952 distance: 29 - 32: 27.033 distance: 30 - 31: 9.447 distance: 30 - 36: 18.197 distance: 31 - 65: 38.692 distance: 33 - 34: 12.013 distance: 33 - 35: 10.491 distance: 36 - 37: 27.101 distance: 37 - 38: 25.154 distance: 37 - 40: 30.321 distance: 38 - 39: 22.856 distance: 38 - 48: 13.206 distance: 39 - 72: 26.069 distance: 40 - 41: 17.596 distance: 41 - 42: 9.875 distance: 41 - 43: 30.100 distance: 42 - 44: 25.982 distance: 43 - 45: 17.139 distance: 44 - 46: 40.853 distance: 48 - 49: 44.970 distance: 49 - 50: 10.918 distance: 49 - 52: 24.368 distance: 50 - 56: 10.523 distance: 51 - 81: 46.365 distance: 52 - 53: 59.104 distance: 52 - 54: 38.936 distance: 53 - 55: 12.738 distance: 56 - 57: 11.628 distance: 57 - 58: 4.116 distance: 57 - 60: 21.359 distance: 58 - 59: 6.624 distance: 58 - 65: 7.422 distance: 60 - 61: 19.117 distance: 61 - 62: 14.447 distance: 63 - 64: 53.268 distance: 66 - 67: 12.323 distance: 66 - 69: 53.223 distance: 67 - 68: 20.037 distance: 67 - 72: 22.685 distance: 69 - 70: 33.111 distance: 69 - 71: 17.443 distance: 72 - 73: 31.918 distance: 74 - 75: 41.115 distance: 74 - 81: 40.265 distance: 76 - 77: 37.416 distance: 77 - 78: 29.292 distance: 78 - 79: 8.674 distance: 81 - 82: 23.535 distance: 82 - 83: 22.195 distance: 82 - 85: 15.619 distance: 84 - 111: 36.361 distance: 85 - 86: 37.678 distance: 85 - 87: 37.260 distance: 86 - 88: 44.141 distance: 89 - 90: 25.091 distance: 90 - 91: 33.226 distance: 90 - 93: 11.391 distance: 91 - 97: 40.092 distance: 92 - 118: 35.039 distance: 93 - 94: 19.000 distance: 94 - 95: 17.685 distance: 97 - 98: 40.782 distance: 97 - 103: 17.139 distance: 98 - 99: 31.512 distance: 98 - 101: 16.138 distance: 99 - 100: 29.102 distance: 99 - 104: 20.775 distance: 100 - 128: 33.408 distance: 101 - 102: 15.433 distance: 102 - 103: 41.776