Starting phenix.real_space_refine on Wed Nov 22 04:30:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4a_17403/11_2023/8p4a_17403.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4a_17403/11_2023/8p4a_17403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4a_17403/11_2023/8p4a_17403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4a_17403/11_2023/8p4a_17403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4a_17403/11_2023/8p4a_17403.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4a_17403/11_2023/8p4a_17403.pdb" } resolution = 3.6 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= 0.001 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 86 5.49 5 Mg 1 5.21 5 S 222 5.16 5 C 22912 2.51 5 N 6426 2.21 5 O 7018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A GLU 936": "OE1" <-> "OE2" Residue "A GLU 1085": "OE1" <-> "OE2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1280": "OD1" <-> "OD2" Residue "A PHE 1471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1056": "OD1" <-> "OD2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 21": "OE1" <-> "OE2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 66": "OD1" <-> "OD2" Residue "M PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 101": "OE1" <-> "OE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M GLU 172": "OE1" <-> "OE2" Residue "M PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 182": "OE1" <-> "OE2" Residue "M TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 495": "OE1" <-> "OE2" Residue "M PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 511": "OD1" <-> "OD2" Residue "M GLU 516": "OE1" <-> "OE2" Residue "M PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 520": "OE1" <-> "OE2" Residue "M PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 36673 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11142 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1337} Chain breaks: 3 Chain: "P" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 405 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "B" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8928 Classifications: {'peptide': 1116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1062} Chain breaks: 6 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2070 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 998 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1305 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 591 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 Chain: "T" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 785 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "M" Number of atoms: 4083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4083 Classifications: {'peptide': 507} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 477} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" 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 768 SG CYS A 111 100.182 55.697 135.873 1.00194.06 S ATOM 796 SG CYS A 114 103.497 53.982 137.853 1.00204.54 S ATOM 464 SG CYS A 71 111.340 68.027 91.175 1.00167.86 S ATOM 486 SG CYS A 74 109.892 64.857 89.530 1.00164.59 S ATOM 533 SG CYS A 81 107.518 67.750 90.273 1.00154.12 S ATOM 20044 SG CYS B1119 106.846 52.672 98.178 1.00160.36 S ATOM 20066 SG CYS B1122 106.866 53.229 100.989 1.00150.21 S ATOM 20181 SG CYS B1137 108.911 54.983 98.807 1.00164.49 S ATOM 21168 SG CYS C 88 76.439 90.574 36.043 1.00180.61 S ATOM 21181 SG CYS C 90 79.033 92.113 38.399 1.00189.59 S ATOM 21216 SG CYS C 94 76.912 94.255 36.084 1.00161.86 S ATOM 21238 SG CYS C 97 75.398 92.618 39.154 1.00161.06 S ATOM 28482 SG CYS I 17 56.334 100.268 158.172 1.00197.04 S ATOM 28506 SG CYS I 20 59.763 100.505 156.556 1.00199.23 S ATOM 28667 SG CYS I 39 58.693 97.154 157.602 1.00196.03 S ATOM 28692 SG CYS I 42 59.295 99.841 160.300 1.00204.97 S ATOM 29044 SG CYS I 86 23.618 105.453 128.447 1.00168.40 S ATOM 29068 SG CYS I 89 23.352 108.306 127.868 1.00178.30 S ATOM 29272 SG CYS I 114 25.481 106.905 125.512 1.00176.35 S ATOM 29307 SG CYS I 119 26.789 108.780 128.157 1.00181.99 S ATOM 29418 SG CYS J 7 52.080 97.206 59.754 1.00127.09 S ATOM 29442 SG CYS J 10 49.597 95.461 57.056 1.00133.91 S ATOM 29706 SG CYS J 44 48.471 95.930 60.349 1.00137.18 S ATOM 29712 SG CYS J 45 49.318 98.997 58.062 1.00136.71 S ATOM 30893 SG CYS L 22 88.160 122.559 73.849 1.00175.09 S ATOM 31010 SG CYS L 36 91.310 121.403 73.461 1.00175.60 S Time building chain proxies: 19.03, per 1000 atoms: 0.52 Number of scatterers: 36673 At special positions: 0 Unit cell: (166.95, 140.7, 180.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 222 16.00 P 86 15.00 Mg 1 11.99 O 7018 8.00 N 6426 7.00 C 22912 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: 14.34 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1122 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1137 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1119 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 39 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 27 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB MET M 30 " Number of C-beta restraints generated: 8216 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 53 sheets defined 37.3% alpha, 18.5% beta 25 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 11.99 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 98 through 110 removed outlier: 4.150A pdb=" N LYS A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.598A pdb=" N LYS A 149 " --> pdb=" O TYR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.570A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.586A pdb=" N MET A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 248' Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.644A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.381A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.154A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 4.082A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.835A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.914A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 757 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.726A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.802A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 4.049A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1160 Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.733A pdb=" N TRP A1192 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A1194 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1224 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.607A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1296 removed outlier: 4.163A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A1296 " --> pdb=" O MET A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.898A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.625A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1435 through 1445 Processing helix chain 'A' and resid 1454 through 1461 Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.135A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.178A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 4.093A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 4.111A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 335 through 346 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.730A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 removed outlier: 4.528A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 583 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.617A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.641A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.603A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.511A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 711 removed outlier: 3.740A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 711' Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.879A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.611A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.639A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.557A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.752A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.600A pdb=" N GLN D 19 " --> pdb=" O ASP D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.664A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR D 28 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.678A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.827A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 97 removed outlier: 4.039A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.587A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 137' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.515A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.507A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.822A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.535A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.056A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 6 through 10 removed outlier: 3.954A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 10' Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.602A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 removed outlier: 3.513A pdb=" N GLU K 114 " --> pdb=" O LYS K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 23 Processing helix chain 'M' and resid 19 through 22 Processing helix chain 'M' and resid 32 through 37 removed outlier: 4.184A pdb=" N SER M 37 " --> pdb=" O PRO M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 53 removed outlier: 4.289A pdb=" N TYR M 53 " --> pdb=" O MET M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 57 Processing helix chain 'M' and resid 76 through 83 removed outlier: 3.513A pdb=" N GLU M 80 " --> pdb=" O ARG M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 117 removed outlier: 4.227A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG M 116 " --> pdb=" O ARG M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 144 Processing helix chain 'M' and resid 148 through 160 removed outlier: 3.759A pdb=" N VAL M 153 " --> pdb=" O ILE M 149 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE M 156 " --> pdb=" O ALA M 152 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA M 157 " --> pdb=" O VAL M 153 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN M 158 " --> pdb=" O ALA M 154 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA M 159 " --> pdb=" O THR M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 178 Processing helix chain 'M' and resid 246 through 262 removed outlier: 3.537A pdb=" N GLU M 252 " --> pdb=" O PRO M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 286 removed outlier: 3.504A pdb=" N LEU M 286 " --> pdb=" O LEU M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 371 through 375 Processing helix chain 'M' and resid 376 through 388 Processing helix chain 'M' and resid 388 through 398 removed outlier: 3.558A pdb=" N ARG M 392 " --> pdb=" O ILE M 388 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR M 398 " --> pdb=" O GLU M 394 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 425 removed outlier: 4.370A pdb=" N LEU M 424 " --> pdb=" O SER M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 504 through 510 removed outlier: 4.180A pdb=" N TYR M 510 " --> pdb=" O GLU M 506 " (cutoff:3.500A) Processing helix chain 'M' and resid 538 through 549 Processing helix chain 'M' and resid 554 through 564 removed outlier: 5.006A pdb=" N GLU M 560 " --> pdb=" O GLU M 556 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N PHE M 561 " --> pdb=" O MET M 557 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.542A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.696A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 5.812A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.772A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.140A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.979A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.205A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.205A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.881A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB8, first strand: chain 'A' and resid 1308 through 1310 Processing sheet with id=AB9, first strand: chain 'A' and resid 1243 through 1246 removed outlier: 3.674A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC2, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.317A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AC5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.286A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.714A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 223 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD1, first strand: chain 'B' and resid 550 through 552 removed outlier: 5.293A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.633A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.633A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD5, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD6, first strand: chain 'B' and resid 865 through 867 removed outlier: 7.231A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD8, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.905A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.293A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 50 " --> pdb=" O PHE L 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.616A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 30 through 31 removed outlier: 6.750A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AE5, first strand: chain 'E' and resid 102 through 106 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 5.722A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.531A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AE9, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.707A pdb=" N VAL H 141 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY H 94 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.852A pdb=" N TYR I 37 " --> pdb=" O GLN I 46 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN I 46 " --> pdb=" O TYR I 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF4, first strand: chain 'M' and resid 24 through 26 removed outlier: 3.577A pdb=" N VAL M 124 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU M 64 " --> pdb=" O ILE M 87 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU M 89 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP M 66 " --> pdb=" O LEU M 89 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N CYS M 91 " --> pdb=" O ASP M 66 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR M 68 " --> pdb=" O CYS M 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 241 through 243 removed outlier: 4.261A pdb=" N VAL M 310 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE M 311 " --> pdb=" O LEU M 303 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU M 341 " --> pdb=" O ILE M 364 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE M 364 " --> pdb=" O LEU M 341 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASP M 343 " --> pdb=" O TYR M 362 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 271 through 275 removed outlier: 4.184A pdb=" N VAL M 274 " --> pdb=" O CYS M 453 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP M 455 " --> pdb=" O VAL M 274 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N ASP M 455 " --> pdb=" O PRO M 444 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU M 457 " --> pdb=" O PHE M 442 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 466 through 470 removed outlier: 4.091A pdb=" N VAL M 467 " --> pdb=" O CYS M 517 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU M 516 " --> pdb=" O MET M 527 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 472 through 476 removed outlier: 7.681A pdb=" N VAL M 491 " --> pdb=" O PRO M 497 " (cutoff:3.500A) 1445 hydrogen bonds defined for protein. 3951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 18.60 Time building geometry restraints manager: 15.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6002 1.31 - 1.44: 9900 1.44 - 1.56: 21133 1.56 - 1.69: 169 1.69 - 1.81: 351 Bond restraints: 37555 Sorted by residual: bond pdb=" C GLN M 18 " pdb=" N PRO M 19 " ideal model delta sigma weight residual 1.333 1.733 -0.401 1.17e-02 7.31e+03 1.17e+03 bond pdb=" N LYS M 28 " pdb=" CA LYS M 28 " ideal model delta sigma weight residual 1.457 1.531 -0.074 1.29e-02 6.01e+03 3.29e+01 bond pdb=" C LEU M 31 " pdb=" O LEU M 31 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.26e-02 6.30e+03 1.53e+01 bond pdb=" N LEU M 27 " pdb=" CA LEU M 27 " ideal model delta sigma weight residual 1.451 1.511 -0.060 1.62e-02 3.81e+03 1.36e+01 bond pdb=" N ARG M 564 " pdb=" CA ARG M 564 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.25e+01 ... (remaining 37550 not shown) Histogram of bond angle deviations from ideal: 95.22 - 103.06: 434 103.06 - 110.90: 13819 110.90 - 118.74: 16974 118.74 - 126.58: 19183 126.58 - 134.42: 699 Bond angle restraints: 51109 Sorted by residual: angle pdb=" N MET M 30 " pdb=" CA MET M 30 " pdb=" C MET M 30 " ideal model delta sigma weight residual 110.35 129.95 -19.60 1.36e+00 5.41e-01 2.08e+02 angle pdb=" N PRO M 118 " pdb=" CA PRO M 118 " pdb=" C PRO M 118 " ideal model delta sigma weight residual 110.70 123.65 -12.95 1.22e+00 6.72e-01 1.13e+02 angle pdb=" N LYS M 28 " pdb=" CA LYS M 28 " pdb=" CB LYS M 28 " ideal model delta sigma weight residual 110.49 97.93 12.56 1.69e+00 3.50e-01 5.53e+01 angle pdb=" C ARG M 132 " pdb=" CA ARG M 132 " pdb=" CB ARG M 132 " ideal model delta sigma weight residual 109.83 117.14 -7.31 9.90e-01 1.02e+00 5.45e+01 angle pdb=" CA LEU M 27 " pdb=" C LEU M 27 " pdb=" O LEU M 27 " ideal model delta sigma weight residual 120.77 113.07 7.70 1.06e+00 8.90e-01 5.28e+01 ... (remaining 51104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 21894 33.25 - 66.49: 725 66.49 - 99.74: 52 99.74 - 132.98: 2 132.98 - 166.23: 5 Dihedral angle restraints: 22678 sinusoidal: 9974 harmonic: 12704 Sorted by residual: dihedral pdb=" CA PHE M 416 " pdb=" C PHE M 416 " pdb=" N ASP M 417 " pdb=" CA ASP M 417 " ideal model delta harmonic sigma weight residual -180.00 -123.23 -56.77 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" C CYS M 13 " pdb=" N CYS M 13 " pdb=" CA CYS M 13 " pdb=" CB CYS M 13 " ideal model delta harmonic sigma weight residual -122.60 -150.46 27.86 0 2.50e+00 1.60e-01 1.24e+02 dihedral pdb=" N CYS M 13 " pdb=" C CYS M 13 " pdb=" CA CYS M 13 " pdb=" CB CYS M 13 " ideal model delta harmonic sigma weight residual 122.80 150.18 -27.38 0 2.50e+00 1.60e-01 1.20e+02 ... (remaining 22675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.941: 5705 0.941 - 1.882: 1 1.882 - 2.824: 0 2.824 - 3.765: 0 3.765 - 4.706: 1 Chirality restraints: 5707 Sorted by residual: chirality pdb=" CA MET M 30 " pdb=" N MET M 30 " pdb=" C MET M 30 " pdb=" CB MET M 30 " both_signs ideal model delta sigma weight residual False 2.51 -2.20 4.71 2.00e-01 2.50e+01 5.54e+02 chirality pdb=" CA CYS M 13 " pdb=" N CYS M 13 " pdb=" C CYS M 13 " pdb=" CB CYS M 13 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.15 2.00e-01 2.50e+01 3.28e+01 chirality pdb=" CA ARG M 132 " pdb=" N ARG M 132 " pdb=" C ARG M 132 " pdb=" CB ARG M 132 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.96e+01 ... (remaining 5704 not shown) Planarity restraints: 6328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN M 18 " 0.040 2.00e-02 2.50e+03 7.08e-02 5.02e+01 pdb=" C GLN M 18 " -0.122 2.00e-02 2.50e+03 pdb=" O GLN M 18 " 0.047 2.00e-02 2.50e+03 pdb=" N PRO M 19 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1102 " -0.029 2.00e-02 2.50e+03 5.74e-02 3.29e+01 pdb=" C MET A1102 " 0.099 2.00e-02 2.50e+03 pdb=" O MET A1102 " -0.038 2.00e-02 2.50e+03 pdb=" N THR A1103 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS M 28 " 0.027 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C LYS M 28 " -0.095 2.00e-02 2.50e+03 pdb=" O LYS M 28 " 0.036 2.00e-02 2.50e+03 pdb=" N THR M 29 " 0.032 2.00e-02 2.50e+03 ... (remaining 6325 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 294 2.55 - 3.14: 29611 3.14 - 3.72: 60513 3.72 - 4.31: 84191 4.31 - 4.90: 136185 Nonbonded interactions: 310794 Sorted by model distance: nonbonded pdb=" O LEU D 86 " pdb=" NZ LYS D 90 " model vdw 1.959 2.520 nonbonded pdb=" OP1 A P 44 " pdb=" O3' A P 44 " model vdw 2.058 3.040 nonbonded pdb=" OG1 THR F 58 " pdb=" OE1 GLU F 61 " model vdw 2.066 2.440 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.085 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2001 " model vdw 2.094 2.170 ... (remaining 310789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.940 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: 0.040 Extract box with map and model: 7.960 Check model and map are aligned: 0.560 Set scattering table: 0.320 Process input model: 109.700 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 : 0.005 0.401 37555 Z= 0.276 Angle : 0.838 19.604 51109 Z= 0.532 Chirality : 0.090 4.706 5707 Planarity : 0.005 0.101 6328 Dihedral : 15.162 166.227 14462 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.58 % Favored : 95.23 % Rotamer: Outliers : 3.72 % Allowed : 1.59 % Favored : 94.69 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.87 (0.13), residues: 4319 helix: 0.63 (0.14), residues: 1435 sheet: -1.29 (0.19), residues: 667 loop : -1.13 (0.13), residues: 2217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 253 time to evaluate : 4.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 53 residues processed: 391 average time/residue: 0.5644 time to fit residues: 348.5141 Evaluate side-chains 255 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 202 time to evaluate : 4.297 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 3 residues processed: 53 average time/residue: 0.5757 time to fit residues: 53.1961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 395 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN A 704 ASN A 791 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 HIS ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN B 649 ASN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN B1133 HIS E 107 GLN E 148 HIS ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 255 GLN M 280 ASN ** M 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 ASN M 547 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 37555 Z= 0.390 Angle : 0.732 12.555 51109 Z= 0.380 Chirality : 0.046 0.560 5707 Planarity : 0.006 0.183 6328 Dihedral : 14.282 174.488 5665 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer: Outliers : 1.15 % Allowed : 7.66 % Favored : 91.20 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.63 (0.13), residues: 4319 helix: 0.81 (0.14), residues: 1455 sheet: -1.26 (0.20), residues: 615 loop : -0.96 (0.13), residues: 2249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 215 time to evaluate : 4.021 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 outliers start: 44 outliers final: 22 residues processed: 245 average time/residue: 0.4795 time to fit residues: 200.0395 Evaluate side-chains 213 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 4.191 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3881 time to fit residues: 20.9288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 328 optimal weight: 50.0000 chunk 268 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 395 optimal weight: 8.9990 chunk 427 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 392 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 317 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 449 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN C 66 HIS I 46 GLN J 52 HIS K 89 ASN M 90 GLN M 102 ASN M 114 ASN ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN ** M 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37555 Z= 0.342 Angle : 0.673 15.657 51109 Z= 0.349 Chirality : 0.044 0.214 5707 Planarity : 0.005 0.085 6328 Dihedral : 14.195 170.483 5665 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 1.51 % Allowed : 9.46 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.43 (0.13), residues: 4319 helix: 1.05 (0.14), residues: 1444 sheet: -1.15 (0.19), residues: 656 loop : -0.88 (0.14), residues: 2219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 201 time to evaluate : 4.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 18 residues processed: 249 average time/residue: 0.4599 time to fit residues: 196.7501 Evaluate side-chains 203 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 4.339 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3534 time to fit residues: 17.9860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 390 optimal weight: 20.0000 chunk 297 optimal weight: 0.0670 chunk 205 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 397 optimal weight: 3.9990 chunk 420 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 376 optimal weight: 5.9990 chunk 113 optimal weight: 0.0010 overall best weight: 1.1928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN A 441 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN ** M 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 547 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37555 Z= 0.171 Angle : 0.606 11.562 51109 Z= 0.311 Chirality : 0.043 0.223 5707 Planarity : 0.004 0.040 6328 Dihedral : 14.081 174.590 5665 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.63 % Favored : 95.32 % Rotamer: Outliers : 1.02 % Allowed : 10.65 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.32 (0.13), residues: 4319 helix: 1.13 (0.14), residues: 1454 sheet: -1.04 (0.19), residues: 664 loop : -0.82 (0.14), residues: 2201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 205 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 12 residues processed: 238 average time/residue: 0.4870 time to fit residues: 198.3781 Evaluate side-chains 200 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 4.100 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3481 time to fit residues: 13.3951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 350 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 313 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 chunk 290 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 214 optimal weight: 0.4980 chunk 377 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 441 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** M 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 37555 Z= 0.306 Angle : 0.646 17.016 51109 Z= 0.329 Chirality : 0.043 0.245 5707 Planarity : 0.004 0.042 6328 Dihedral : 13.987 174.863 5665 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 1.17 % Allowed : 11.57 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.22 (0.13), residues: 4319 helix: 1.26 (0.14), residues: 1446 sheet: -1.01 (0.19), residues: 688 loop : -0.78 (0.14), residues: 2185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 4.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 18 residues processed: 222 average time/residue: 0.4986 time to fit residues: 193.1998 Evaluate side-chains 198 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 4.519 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3525 time to fit residues: 17.6052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 141 optimal weight: 8.9990 chunk 378 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 420 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS K 89 ASN ** M 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 37555 Z= 0.281 Angle : 0.631 11.258 51109 Z= 0.324 Chirality : 0.043 0.221 5707 Planarity : 0.004 0.040 6328 Dihedral : 13.937 176.434 5665 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 1.20 % Allowed : 12.48 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.13), residues: 4319 helix: 1.27 (0.14), residues: 1442 sheet: -1.01 (0.19), residues: 693 loop : -0.73 (0.14), residues: 2184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 4.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 12 residues processed: 228 average time/residue: 0.4614 time to fit residues: 181.6973 Evaluate side-chains 196 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 4.223 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3242 time to fit residues: 13.7865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 307 optimal weight: 0.3980 chunk 238 optimal weight: 6.9990 chunk 354 optimal weight: 30.0000 chunk 235 optimal weight: 0.0670 chunk 419 optimal weight: 20.0000 chunk 262 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 overall best weight: 2.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 HIS ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37555 Z= 0.198 Angle : 0.625 12.119 51109 Z= 0.317 Chirality : 0.043 0.215 5707 Planarity : 0.004 0.037 6328 Dihedral : 13.884 178.058 5665 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 0.91 % Allowed : 13.41 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.13 (0.13), residues: 4319 helix: 1.28 (0.14), residues: 1442 sheet: -0.95 (0.19), residues: 677 loop : -0.68 (0.14), residues: 2200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 4.681 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 outliers start: 35 outliers final: 15 residues processed: 221 average time/residue: 0.4947 time to fit residues: 186.7272 Evaluate side-chains 201 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 4.380 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4939 time to fit residues: 18.7610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 259 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 chunk 207 optimal weight: 0.0050 chunk 39 optimal weight: 9.9990 chunk 329 optimal weight: 0.5980 overall best weight: 2.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 377 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37555 Z= 0.211 Angle : 0.634 11.263 51109 Z= 0.320 Chirality : 0.043 0.211 5707 Planarity : 0.004 0.042 6328 Dihedral : 13.799 179.460 5665 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 0.60 % Allowed : 13.83 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.06 (0.13), residues: 4319 helix: 1.31 (0.14), residues: 1446 sheet: -0.86 (0.19), residues: 678 loop : -0.64 (0.14), residues: 2195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 4.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 205 average time/residue: 0.4873 time to fit residues: 171.9968 Evaluate side-chains 194 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 185 time to evaluate : 4.176 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3533 time to fit residues: 11.5947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 381 optimal weight: 10.0000 chunk 401 optimal weight: 50.0000 chunk 366 optimal weight: 10.0000 chunk 390 optimal weight: 30.0000 chunk 235 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 369 optimal weight: 7.9990 chunk 389 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 377 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN B 197 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN C 83 GLN E 30 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 547 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 37555 Z= 0.361 Angle : 0.714 13.359 51109 Z= 0.358 Chirality : 0.044 0.220 5707 Planarity : 0.004 0.040 6328 Dihedral : 13.820 179.509 5665 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.58 % Favored : 94.37 % Rotamer: Outliers : 0.31 % Allowed : 14.25 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.12 (0.13), residues: 4319 helix: 1.29 (0.14), residues: 1442 sheet: -0.87 (0.20), residues: 635 loop : -0.72 (0.14), residues: 2242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 197 average time/residue: 0.5121 time to fit residues: 174.1866 Evaluate side-chains 189 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 4.208 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3465 time to fit residues: 7.7253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 256 optimal weight: 6.9990 chunk 413 optimal weight: 40.0000 chunk 252 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 433 optimal weight: 9.9990 chunk 398 optimal weight: 6.9990 chunk 345 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 37555 Z= 0.295 Angle : 0.689 14.067 51109 Z= 0.345 Chirality : 0.043 0.193 5707 Planarity : 0.004 0.043 6328 Dihedral : 13.806 177.117 5665 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 0.13 % Allowed : 14.72 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.11 (0.13), residues: 4319 helix: 1.27 (0.14), residues: 1447 sheet: -0.90 (0.19), residues: 672 loop : -0.67 (0.14), residues: 2200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 195 average time/residue: 0.4918 time to fit residues: 164.4368 Evaluate side-chains 190 residues out of total 3880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 4.450 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3749 time to fit residues: 7.3999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 274 optimal weight: 10.0000 chunk 367 optimal weight: 9.9990 chunk 105 optimal weight: 0.0010 chunk 318 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 345 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 354 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 overall best weight: 1.1768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 293 ASN A 377 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1313 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.049035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.032456 restraints weight = 242630.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.033561 restraints weight = 119543.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.034289 restraints weight = 75054.444| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37555 Z= 0.172 Angle : 0.658 13.411 51109 Z= 0.327 Chirality : 0.043 0.194 5707 Planarity : 0.004 0.038 6328 Dihedral : 13.717 172.998 5665 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 0.16 % Allowed : 14.93 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.04 (0.13), residues: 4319 helix: 1.30 (0.14), residues: 1447 sheet: -0.81 (0.20), residues: 664 loop : -0.62 (0.14), residues: 2208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5956.46 seconds wall clock time: 111 minutes 50.43 seconds (6710.43 seconds total)