Starting phenix.real_space_refine (version: dev) on Mon May 16 02:03:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/05_2022/7pxh_13703_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/05_2022/7pxh_13703.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/05_2022/7pxh_13703_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/05_2022/7pxh_13703_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/05_2022/7pxh_13703_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/05_2022/7pxh_13703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/05_2022/7pxh_13703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/05_2022/7pxh_13703_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/05_2022/7pxh_13703_updated.pdb" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A ASP 911": "OD1" <-> "OD2" Residue "A TYR 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B ASP 911": "OD1" <-> "OD2" Residue "B TYR 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 386": "OD1" <-> "OD2" Residue "C ASP 451": "OD1" <-> "OD2" Residue "C ASP 892": "OD1" <-> "OD2" Residue "C TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1038": "OE1" <-> "OE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D ASP 451": "OD1" <-> "OD2" Residue "D ASP 892": "OD1" <-> "OD2" Residue "D TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1038": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 28922 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "B" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "C" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "D" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "A" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 191 Unusual residues: {' K': 5, '6PL': 4, ' CA': 2, ' MG': 1, 'CLR': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 51 Chain: "B" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 266 Unusual residues: {'6PL': 4, '8I2': 1, ' CA': 2, ' MG': 1, 'CLR': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 51 Chain: "C" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 187 Unusual residues: {' K': 1, '6PL': 4, ' CA': 2, ' MG': 1, 'CLR': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 51 Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 186 Unusual residues: {'6PL': 4, ' CA': 2, ' MG': 1, 'CLR': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 51 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" K K A1209 " occ=0.50 residue: pdb=" K K A1210 " occ=0.50 residue: pdb=" K K A1211 " occ=0.50 residue: pdb=" K K A1212 " occ=0.50 residue: pdb=" K K A1213 " occ=0.25 residue: pdb=" K K C1209 " occ=0.25 Time building chain proxies: 16.73, per 1000 atoms: 0.58 Number of scatterers: 28922 At special positions: 0 Unit cell: (165.9, 165.9, 128.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 K 6 19.00 S 192 16.00 P 16 15.00 Mg 4 11.99 O 5262 8.00 N 4610 7.00 C 18824 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.72 Conformation dependent library (CDL) restraints added in 4.2 seconds 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 16 sheets defined 48.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 49 through 76 removed outlier: 3.831A pdb=" N VAL A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.867A pdb=" N ASP A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 148 removed outlier: 3.762A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 185 removed outlier: 3.886A pdb=" N PHE A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 196 through 202 removed outlier: 3.858A pdb=" N VAL A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 removed outlier: 3.658A pdb=" N PHE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 238 removed outlier: 3.641A pdb=" N ARG A 225 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 245 through 274 Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.514A pdb=" N PHE A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.775A pdb=" N ASP A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 447 through 464 Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.902A pdb=" N ALA A 481 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 513 removed outlier: 3.588A pdb=" N LEU A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 525 removed outlier: 4.100A pdb=" N PHE A 525 " --> pdb=" O MET A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 547 Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 618 through 625 removed outlier: 4.265A pdb=" N ARG A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TRP A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 801 through 806 Processing helix chain 'A' and resid 828 through 836 removed outlier: 4.805A pdb=" N MET A 833 " --> pdb=" O ASN A 830 " (cutoff:3.500A) Proline residue: A 834 - end of helix Processing helix chain 'A' and resid 854 through 863 removed outlier: 3.846A pdb=" N ARG A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N MET A 863 " --> pdb=" O ARG A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 886 Processing helix chain 'A' and resid 907 through 923 removed outlier: 4.096A pdb=" N ASP A 911 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU A 913 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 914 " --> pdb=" O ASP A 911 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 915 " --> pdb=" O LYS A 912 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 921 " --> pdb=" O SER A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 973 through 978 removed outlier: 3.563A pdb=" N VAL A 976 " --> pdb=" O ASP A 973 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN A 977 " --> pdb=" O GLY A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 993 No H-bonds generated for 'chain 'A' and resid 991 through 993' Processing helix chain 'A' and resid 995 through 998 No H-bonds generated for 'chain 'A' and resid 995 through 998' Processing helix chain 'A' and resid 1005 through 1017 removed outlier: 3.580A pdb=" N ASP A1009 " --> pdb=" O SER A1006 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER A1010 " --> pdb=" O VAL A1007 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A1012 " --> pdb=" O ASP A1009 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A1015 " --> pdb=" O MET A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1029 Processing helix chain 'A' and resid 1035 through 1043 Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1076 through 1080 removed outlier: 4.078A pdb=" N GLU A1080 " --> pdb=" O GLN A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1095 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.831A pdb=" N VAL B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.866A pdb=" N ASP B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 148 removed outlier: 3.761A pdb=" N ILE B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 185 removed outlier: 3.886A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.859A pdb=" N VAL B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.658A pdb=" N PHE B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 238 removed outlier: 3.641A pdb=" N ARG B 225 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 245 through 274 Processing helix chain 'B' and resid 288 through 299 Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.514A pdb=" N PHE B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.775A pdb=" N ASP B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 377 Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 447 through 464 Processing helix chain 'B' and resid 477 through 484 removed outlier: 3.901A pdb=" N ALA B 481 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 513 removed outlier: 3.586A pdb=" N LEU B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 525 removed outlier: 4.100A pdb=" N PHE B 525 " --> pdb=" O MET B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 547 Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 565 through 575 Processing helix chain 'B' and resid 618 through 625 removed outlier: 4.265A pdb=" N ARG B 623 " --> pdb=" O ASP B 619 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP B 625 " --> pdb=" O VAL B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 797 No H-bonds generated for 'chain 'B' and resid 795 through 797' Processing helix chain 'B' and resid 801 through 806 Processing helix chain 'B' and resid 828 through 836 removed outlier: 4.805A pdb=" N MET B 833 " --> pdb=" O ASN B 830 " (cutoff:3.500A) Proline residue: B 834 - end of helix Processing helix chain 'B' and resid 854 through 863 removed outlier: 3.846A pdb=" N ARG B 859 " --> pdb=" O ASP B 855 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS B 862 " --> pdb=" O ARG B 858 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N MET B 863 " --> pdb=" O ARG B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 886 Processing helix chain 'B' and resid 907 through 923 removed outlier: 4.096A pdb=" N ASP B 911 " --> pdb=" O THR B 908 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU B 913 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 914 " --> pdb=" O ASP B 911 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 915 " --> pdb=" O LYS B 912 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 921 " --> pdb=" O SER B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 963 No H-bonds generated for 'chain 'B' and resid 961 through 963' Processing helix chain 'B' and resid 973 through 978 removed outlier: 3.563A pdb=" N VAL B 976 " --> pdb=" O ASP B 973 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN B 977 " --> pdb=" O GLY B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 993 No H-bonds generated for 'chain 'B' and resid 991 through 993' Processing helix chain 'B' and resid 995 through 998 No H-bonds generated for 'chain 'B' and resid 995 through 998' Processing helix chain 'B' and resid 1005 through 1017 removed outlier: 3.581A pdb=" N ASP B1009 " --> pdb=" O SER B1006 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B1010 " --> pdb=" O VAL B1007 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET B1012 " --> pdb=" O ASP B1009 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B1015 " --> pdb=" O MET B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1029 Processing helix chain 'B' and resid 1035 through 1043 Processing helix chain 'B' and resid 1056 through 1060 Processing helix chain 'B' and resid 1076 through 1080 removed outlier: 4.079A pdb=" N GLU B1080 " --> pdb=" O GLN B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1095 Processing helix chain 'C' and resid 49 through 76 removed outlier: 3.670A pdb=" N ARG C 71 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.787A pdb=" N ASP C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 147 removed outlier: 3.775A pdb=" N ILE C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 185 removed outlier: 3.824A pdb=" N PHE C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 196 through 202 removed outlier: 3.583A pdb=" N ASP C 201 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 removed outlier: 3.715A pdb=" N TYR C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 238 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 245 through 274 Processing helix chain 'C' and resid 288 through 299 Processing helix chain 'C' and resid 312 through 340 removed outlier: 3.551A pdb=" N LEU C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Proline residue: C 334 - end of helix Processing helix chain 'C' and resid 367 through 377 removed outlier: 3.507A pdb=" N HIS C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 422 through 428 Processing helix chain 'C' and resid 447 through 464 Processing helix chain 'C' and resid 477 through 484 removed outlier: 3.793A pdb=" N ALA C 481 " --> pdb=" O HIS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 513 removed outlier: 3.628A pdb=" N LEU C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 524 Processing helix chain 'C' and resid 538 through 548 Processing helix chain 'C' and resid 558 through 560 No H-bonds generated for 'chain 'C' and resid 558 through 560' Processing helix chain 'C' and resid 565 through 574 Processing helix chain 'C' and resid 618 through 626 removed outlier: 4.289A pdb=" N ARG C 623 " --> pdb=" O ASP C 619 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP C 625 " --> pdb=" O VAL C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 797 No H-bonds generated for 'chain 'C' and resid 795 through 797' Processing helix chain 'C' and resid 801 through 806 Processing helix chain 'C' and resid 828 through 836 removed outlier: 3.662A pdb=" N LEU C 831 " --> pdb=" O LEU C 828 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N MET C 833 " --> pdb=" O ASN C 830 " (cutoff:3.500A) Proline residue: C 834 - end of helix Processing helix chain 'C' and resid 854 through 860 removed outlier: 3.806A pdb=" N ARG C 859 " --> pdb=" O ASP C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 885 Processing helix chain 'C' and resid 888 through 890 No H-bonds generated for 'chain 'C' and resid 888 through 890' Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 912 through 923 Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 973 through 978 removed outlier: 3.957A pdb=" N GLN C 977 " --> pdb=" O GLY C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 993 No H-bonds generated for 'chain 'C' and resid 991 through 993' Processing helix chain 'C' and resid 995 through 998 No H-bonds generated for 'chain 'C' and resid 995 through 998' Processing helix chain 'C' and resid 1005 through 1017 removed outlier: 3.698A pdb=" N ASP C1009 " --> pdb=" O SER C1006 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER C1010 " --> pdb=" O VAL C1007 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET C1012 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C1013 " --> pdb=" O SER C1010 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR C1015 " --> pdb=" O MET C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1029 Processing helix chain 'C' and resid 1035 through 1043 removed outlier: 3.538A pdb=" N LEU C1039 " --> pdb=" O PRO C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1060 removed outlier: 4.348A pdb=" N ASN C1059 " --> pdb=" O GLU C1055 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG C1060 " --> pdb=" O SER C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1080 removed outlier: 4.090A pdb=" N GLU C1080 " --> pdb=" O GLN C1077 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1094 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.670A pdb=" N ARG D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.786A pdb=" N ASP D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 147 removed outlier: 3.776A pdb=" N ILE D 128 " --> pdb=" O THR D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 185 removed outlier: 3.823A pdb=" N PHE D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 196 through 202 removed outlier: 3.584A pdb=" N ASP D 201 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.716A pdb=" N TYR D 213 " --> pdb=" O PHE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 238 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 245 through 274 Processing helix chain 'D' and resid 288 through 299 Processing helix chain 'D' and resid 312 through 340 removed outlier: 3.552A pdb=" N LEU D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 324 " --> pdb=" O PHE D 320 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA D 327 " --> pdb=" O LEU D 323 " (cutoff:3.500A) Proline residue: D 334 - end of helix Processing helix chain 'D' and resid 367 through 377 removed outlier: 3.508A pdb=" N HIS D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 407 Processing helix chain 'D' and resid 422 through 428 Processing helix chain 'D' and resid 447 through 464 Processing helix chain 'D' and resid 477 through 484 removed outlier: 3.793A pdb=" N ALA D 481 " --> pdb=" O HIS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 513 removed outlier: 3.628A pdb=" N LEU D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 524 Processing helix chain 'D' and resid 538 through 548 Processing helix chain 'D' and resid 558 through 560 No H-bonds generated for 'chain 'D' and resid 558 through 560' Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 618 through 626 removed outlier: 4.289A pdb=" N ARG D 623 " --> pdb=" O ASP D 619 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA D 624 " --> pdb=" O GLU D 620 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TRP D 625 " --> pdb=" O VAL D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 797 No H-bonds generated for 'chain 'D' and resid 795 through 797' Processing helix chain 'D' and resid 801 through 806 Processing helix chain 'D' and resid 828 through 836 removed outlier: 3.662A pdb=" N LEU D 831 " --> pdb=" O LEU D 828 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N MET D 833 " --> pdb=" O ASN D 830 " (cutoff:3.500A) Proline residue: D 834 - end of helix Processing helix chain 'D' and resid 854 through 860 removed outlier: 3.806A pdb=" N ARG D 859 " --> pdb=" O ASP D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 885 Processing helix chain 'D' and resid 888 through 890 No H-bonds generated for 'chain 'D' and resid 888 through 890' Processing helix chain 'D' and resid 907 through 909 No H-bonds generated for 'chain 'D' and resid 907 through 909' Processing helix chain 'D' and resid 912 through 923 Processing helix chain 'D' and resid 961 through 963 No H-bonds generated for 'chain 'D' and resid 961 through 963' Processing helix chain 'D' and resid 973 through 978 removed outlier: 3.957A pdb=" N GLN D 977 " --> pdb=" O GLY D 974 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 993 No H-bonds generated for 'chain 'D' and resid 991 through 993' Processing helix chain 'D' and resid 995 through 998 No H-bonds generated for 'chain 'D' and resid 995 through 998' Processing helix chain 'D' and resid 1005 through 1017 removed outlier: 3.697A pdb=" N ASP D1009 " --> pdb=" O SER D1006 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER D1010 " --> pdb=" O VAL D1007 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET D1012 " --> pdb=" O ASP D1009 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D1013 " --> pdb=" O SER D1010 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR D1015 " --> pdb=" O MET D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1029 Processing helix chain 'D' and resid 1035 through 1043 removed outlier: 3.537A pdb=" N LEU D1039 " --> pdb=" O PRO D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1054 through 1060 removed outlier: 4.348A pdb=" N ASN D1059 " --> pdb=" O GLU D1055 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG D1060 " --> pdb=" O SER D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1080 removed outlier: 4.089A pdb=" N GLU D1080 " --> pdb=" O GLN D1077 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1094 Processing sheet with id= A, first strand: chain 'A' and resid 496 through 499 removed outlier: 7.344A pdb=" N HIS A 358 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N LEU A 437 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 360 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 550 through 555 removed outlier: 4.479A pdb=" N GLN A 610 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 582 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE A 614 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 580 " --> pdb=" O ILE A 614 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1002 through 1004 removed outlier: 8.187A pdb=" N PHE A1003 " --> pdb=" O MET A 966 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR A 968 " --> pdb=" O PHE A1003 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS A 894 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLU A 969 " --> pdb=" O CYS A 894 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE A 896 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1064 through 1069 removed outlier: 3.616A pdb=" N GLY A1101 " --> pdb=" O PHE A1137 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A1139 " --> pdb=" O CYS A1099 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS A1099 " --> pdb=" O LEU A1139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 496 through 499 removed outlier: 7.345A pdb=" N HIS B 358 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N LEU B 437 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 360 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 550 through 555 removed outlier: 4.479A pdb=" N GLN B 610 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 582 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE B 614 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 580 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 1002 through 1004 removed outlier: 8.187A pdb=" N PHE B1003 " --> pdb=" O MET B 966 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR B 968 " --> pdb=" O PHE B1003 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS B 894 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLU B 969 " --> pdb=" O CYS B 894 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE B 896 " --> pdb=" O GLU B 969 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 3.616A pdb=" N GLY B1101 " --> pdb=" O PHE B1137 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B1139 " --> pdb=" O CYS B1099 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS B1099 " --> pdb=" O LEU B1139 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 496 through 499 removed outlier: 7.468A pdb=" N HIS C 358 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N LEU C 437 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL C 360 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU C 388 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL C 361 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL C 390 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 550 through 555 removed outlier: 3.574A pdb=" N ALA C 615 " --> pdb=" O GLU C 550 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN C 610 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 582 " --> pdb=" O PHE C 612 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE C 614 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 580 " --> pdb=" O ILE C 614 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 1002 through 1004 removed outlier: 8.142A pdb=" N PHE C1003 " --> pdb=" O MET C 966 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR C 968 " --> pdb=" O PHE C1003 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N CYS C 894 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLU C 969 " --> pdb=" O CYS C 894 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE C 896 " --> pdb=" O GLU C 969 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 1064 through 1069 removed outlier: 3.593A pdb=" N GLY C1101 " --> pdb=" O PHE C1137 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU C1139 " --> pdb=" O CYS C1099 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS C1099 " --> pdb=" O LEU C1139 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C1104 " --> pdb=" O TYR C1119 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 496 through 499 removed outlier: 7.468A pdb=" N HIS D 358 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N LEU D 437 " --> pdb=" O HIS D 358 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 360 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU D 388 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL D 361 " --> pdb=" O GLU D 388 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL D 390 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 550 through 555 removed outlier: 3.574A pdb=" N ALA D 615 " --> pdb=" O GLU D 550 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN D 610 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 582 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE D 614 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU D 580 " --> pdb=" O ILE D 614 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 1002 through 1004 removed outlier: 8.142A pdb=" N PHE D1003 " --> pdb=" O MET D 966 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR D 968 " --> pdb=" O PHE D1003 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS D 894 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLU D 969 " --> pdb=" O CYS D 894 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE D 896 " --> pdb=" O GLU D 969 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 1064 through 1069 removed outlier: 3.592A pdb=" N GLY D1101 " --> pdb=" O PHE D1137 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU D1139 " --> pdb=" O CYS D1099 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS D1099 " --> pdb=" O LEU D1139 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D1104 " --> pdb=" O TYR D1119 " (cutoff:3.500A) 1170 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.66 Time building geometry restraints manager: 13.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4588 1.31 - 1.43: 7716 1.43 - 1.56: 16868 1.56 - 1.68: 68 1.68 - 1.81: 296 Bond restraints: 29536 Sorted by residual: bond pdb=" C34 8I2 B1209 " pdb=" N36 8I2 B1209 " ideal model delta sigma weight residual 1.552 1.362 0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" C24 8I2 B1209 " pdb=" N26 8I2 B1209 " ideal model delta sigma weight residual 1.543 1.356 0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" C14 8I2 B1209 " pdb=" N16 8I2 B1209 " ideal model delta sigma weight residual 1.547 1.365 0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" C4 8I2 B1209 " pdb=" N6 8I2 B1209 " ideal model delta sigma weight residual 1.536 1.363 0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" C9 8I2 B1209 " pdb=" O11 8I2 B1209 " ideal model delta sigma weight residual 1.482 1.337 0.145 2.00e-02 2.50e+03 5.25e+01 ... (remaining 29531 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.72: 716 106.72 - 113.54: 16493 113.54 - 120.36: 10646 120.36 - 127.19: 11862 127.19 - 134.01: 285 Bond angle restraints: 40002 Sorted by residual: angle pdb=" O3P 6PL A1205 " pdb=" P 6PL A1205 " pdb=" O4P 6PL A1205 " ideal model delta sigma weight residual 93.65 109.74 -16.09 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O3P 6PL B1205 " pdb=" P 6PL B1205 " pdb=" O4P 6PL B1205 " ideal model delta sigma weight residual 93.65 109.72 -16.07 3.00e+00 1.11e-01 2.87e+01 angle pdb=" C2 8I2 B1209 " pdb=" C4 8I2 B1209 " pdb=" N6 8I2 B1209 " ideal model delta sigma weight residual 109.85 125.77 -15.92 3.00e+00 1.11e-01 2.82e+01 angle pdb=" O3P 6PL D1206 " pdb=" P 6PL D1206 " pdb=" O4P 6PL D1206 " ideal model delta sigma weight residual 93.65 109.50 -15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O3P 6PL A1206 " pdb=" P 6PL A1206 " pdb=" O4P 6PL A1206 " ideal model delta sigma weight residual 93.65 109.45 -15.80 3.00e+00 1.11e-01 2.78e+01 ... (remaining 39997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.07: 17088 34.07 - 68.14: 331 68.14 - 102.21: 24 102.21 - 136.28: 2 136.28 - 170.35: 1 Dihedral angle restraints: 17446 sinusoidal: 7106 harmonic: 10340 Sorted by residual: dihedral pdb=" C50 8I2 B1209 " pdb=" C51 8I2 B1209 " pdb=" N54 8I2 B1209 " pdb=" C55 8I2 B1209 " ideal model delta sinusoidal sigma weight residual 345.07 174.72 170.35 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C32 8I2 B1209 " pdb=" C29 8I2 B1209 " pdb=" O31 8I2 B1209 " pdb=" O30 8I2 B1209 " ideal model delta sinusoidal sigma weight residual -37.33 87.97 -125.30 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C80 8I2 B1209 " pdb=" C82 8I2 B1209 " pdb=" O81 8I2 B1209 " pdb=" C83 8I2 B1209 " ideal model delta sinusoidal sigma weight residual 52.97 -59.32 112.29 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 17443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4268 0.089 - 0.177: 229 0.177 - 0.266: 21 0.266 - 0.354: 9 0.354 - 0.443: 1 Chirality restraints: 4528 Sorted by residual: chirality pdb=" C37 8I2 B1209 " pdb=" C39 8I2 B1209 " pdb=" C42 8I2 B1209 " pdb=" N36 8I2 B1209 " both_signs ideal model delta sigma weight residual False 2.65 2.21 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" C7 8I2 B1209 " pdb=" C84 8I2 B1209 " pdb=" C9 8I2 B1209 " pdb=" N6 8I2 B1209 " both_signs ideal model delta sigma weight residual False -2.66 -2.33 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C14 CLR D1208 " pdb=" C13 CLR D1208 " pdb=" C15 CLR D1208 " pdb=" C8 CLR D1208 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 4525 not shown) Planarity restraints: 4946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 206 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO B 207 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 206 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.35e+00 pdb=" N PRO A 207 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 276 " 0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO D 277 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 277 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 277 " 0.039 5.00e-02 4.00e+02 ... (remaining 4943 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 500 2.69 - 3.30: 32241 3.30 - 3.92: 55334 3.92 - 4.53: 76183 4.53 - 5.14: 116289 Nonbonded interactions: 280547 Sorted by model distance: nonbonded pdb=" O ASN D 523 " pdb="MG MG D1203 " model vdw 2.079 2.170 nonbonded pdb=" O ASN C 523 " pdb="MG MG C1203 " model vdw 2.080 2.170 nonbonded pdb=" O MET C 549 " pdb="MG MG C1203 " model vdw 2.120 2.170 nonbonded pdb=" O MET D 549 " pdb="MG MG D1203 " model vdw 2.120 2.170 nonbonded pdb=" OH TYR A 477 " pdb=" OE1 GLU A1038 " model vdw 2.225 2.440 ... (remaining 280542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 1145 or resid 1201 through 1208)) selection = (chain 'B' and (resid 44 through 1145 or resid 1201 through 1208)) selection = (chain 'C' and (resid 44 through 1145 or resid 1201 through 1208)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 K 6 8.98 5 P 16 5.49 5 Mg 4 5.21 5 S 192 5.16 5 C 18824 2.51 5 N 4610 2.21 5 O 5262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 20.100 Check model and map are aligned: 0.480 Convert atoms to be neutral: 0.260 Process input model: 76.460 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.190 29536 Z= 0.409 Angle : 0.812 16.090 40002 Z= 0.321 Chirality : 0.043 0.443 4528 Planarity : 0.004 0.077 4946 Dihedral : 13.722 170.348 10750 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3492 helix: 0.54 (0.13), residues: 1656 sheet: 0.81 (0.25), residues: 476 loop : 0.49 (0.17), residues: 1360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 425 time to evaluate : 3.305 Fit side-chains outliers start: 14 outliers final: 0 residues processed: 429 average time/residue: 1.1343 time to fit residues: 587.7428 Evaluate side-chains 318 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 3.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 0.4980 chunk 91 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 142 optimal weight: 0.8980 chunk 275 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 319 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 GLN D 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 29536 Z= 0.230 Angle : 0.533 9.818 40002 Z= 0.267 Chirality : 0.042 0.309 4528 Planarity : 0.005 0.079 4946 Dihedral : 9.503 165.094 4234 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3492 helix: 0.73 (0.13), residues: 1640 sheet: 0.51 (0.24), residues: 468 loop : 0.78 (0.18), residues: 1384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 333 time to evaluate : 3.484 Fit side-chains outliers start: 64 outliers final: 32 residues processed: 360 average time/residue: 1.0937 time to fit residues: 480.2592 Evaluate side-chains 335 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 303 time to evaluate : 3.228 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 18 residues processed: 16 average time/residue: 0.5806 time to fit residues: 17.4882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 266 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 345 optimal weight: 4.9990 chunk 285 optimal weight: 0.0070 chunk 317 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN C 372 HIS C 445 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS D 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 29536 Z= 0.422 Angle : 0.583 7.508 40002 Z= 0.293 Chirality : 0.046 0.284 4528 Planarity : 0.005 0.064 4946 Dihedral : 9.754 170.702 4234 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3492 helix: 0.50 (0.12), residues: 1664 sheet: 0.40 (0.25), residues: 420 loop : 0.57 (0.17), residues: 1408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 322 time to evaluate : 3.461 Fit side-chains outliers start: 78 outliers final: 35 residues processed: 367 average time/residue: 1.1703 time to fit residues: 521.7896 Evaluate side-chains 322 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 287 time to evaluate : 3.386 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 25 residues processed: 11 average time/residue: 0.5445 time to fit residues: 13.8657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 321 optimal weight: 4.9990 chunk 340 optimal weight: 0.7980 chunk 167 optimal weight: 0.0060 chunk 304 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN C 372 HIS C 445 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN D 372 HIS D 445 GLN D 995 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 29536 Z= 0.144 Angle : 0.460 8.182 40002 Z= 0.230 Chirality : 0.039 0.290 4528 Planarity : 0.004 0.094 4946 Dihedral : 9.291 169.647 4234 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.14), residues: 3492 helix: 0.68 (0.13), residues: 1696 sheet: 0.34 (0.25), residues: 420 loop : 0.73 (0.18), residues: 1376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 304 time to evaluate : 3.422 Fit side-chains outliers start: 67 outliers final: 45 residues processed: 344 average time/residue: 1.1300 time to fit residues: 474.4296 Evaluate side-chains 330 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 285 time to evaluate : 3.317 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 29 residues processed: 17 average time/residue: 0.9380 time to fit residues: 24.2015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 253 optimal weight: 0.0570 chunk 140 optimal weight: 0.3980 chunk 290 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 305 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS C 172 ASN C 372 HIS C 445 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS D 445 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 29536 Z= 0.346 Angle : 0.523 7.591 40002 Z= 0.263 Chirality : 0.043 0.278 4528 Planarity : 0.005 0.092 4946 Dihedral : 9.360 171.540 4234 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3492 helix: 0.57 (0.12), residues: 1696 sheet: 0.23 (0.25), residues: 420 loop : 0.60 (0.18), residues: 1376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 293 time to evaluate : 3.465 Fit side-chains outliers start: 75 outliers final: 41 residues processed: 335 average time/residue: 1.1358 time to fit residues: 470.6808 Evaluate side-chains 328 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 287 time to evaluate : 3.461 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 29 residues processed: 12 average time/residue: 0.5389 time to fit residues: 13.7925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 340 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 28 optimal weight: 0.0170 chunk 112 optimal weight: 0.6980 chunk 178 optimal weight: 8.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 172 ASN C 372 HIS C 445 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS D 445 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 29536 Z= 0.146 Angle : 0.458 7.779 40002 Z= 0.228 Chirality : 0.039 0.279 4528 Planarity : 0.004 0.090 4946 Dihedral : 9.066 171.140 4234 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3492 helix: 0.78 (0.13), residues: 1700 sheet: 0.24 (0.25), residues: 428 loop : 0.82 (0.18), residues: 1364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 290 time to evaluate : 3.499 Fit side-chains outliers start: 63 outliers final: 43 residues processed: 327 average time/residue: 1.0566 time to fit residues: 425.7902 Evaluate side-chains 320 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 277 time to evaluate : 3.338 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 29 residues processed: 14 average time/residue: 0.7654 time to fit residues: 18.4073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 248 optimal weight: 0.0370 chunk 192 optimal weight: 0.7980 chunk 286 optimal weight: 0.5980 chunk 190 optimal weight: 0.1980 chunk 339 optimal weight: 0.0010 chunk 212 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 156 optimal weight: 0.0370 overall best weight: 0.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 HIS C 172 ASN C 445 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN D 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.099 29536 Z= 0.117 Angle : 0.437 8.222 40002 Z= 0.217 Chirality : 0.039 0.278 4528 Planarity : 0.004 0.091 4946 Dihedral : 8.683 168.556 4234 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3492 helix: 0.98 (0.13), residues: 1692 sheet: 0.27 (0.25), residues: 428 loop : 0.89 (0.18), residues: 1372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 296 time to evaluate : 3.236 Fit side-chains outliers start: 56 outliers final: 35 residues processed: 337 average time/residue: 1.0720 time to fit residues: 445.9868 Evaluate side-chains 317 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 282 time to evaluate : 3.379 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 33 residues processed: 2 average time/residue: 0.3732 time to fit residues: 5.5443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 202 optimal weight: 0.5980 chunk 102 optimal weight: 0.0000 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 215 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 266 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 172 ASN C 372 HIS C 445 GLN D 372 HIS D 445 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 29536 Z= 0.171 Angle : 0.452 8.798 40002 Z= 0.224 Chirality : 0.039 0.274 4528 Planarity : 0.004 0.078 4946 Dihedral : 8.573 168.205 4234 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3492 helix: 1.00 (0.13), residues: 1712 sheet: 0.33 (0.25), residues: 428 loop : 0.87 (0.18), residues: 1352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 285 time to evaluate : 3.542 Fit side-chains outliers start: 62 outliers final: 39 residues processed: 327 average time/residue: 1.1265 time to fit residues: 453.9096 Evaluate side-chains 323 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 284 time to evaluate : 3.511 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 33 residues processed: 6 average time/residue: 0.7341 time to fit residues: 10.2398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 296 optimal weight: 0.0270 chunk 316 optimal weight: 5.9990 chunk 324 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 chunk 299 optimal weight: 0.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 165 GLN C 172 ASN C 372 HIS D 372 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 29536 Z= 0.204 Angle : 0.466 7.716 40002 Z= 0.232 Chirality : 0.040 0.274 4528 Planarity : 0.004 0.072 4946 Dihedral : 8.531 168.944 4234 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3492 helix: 0.97 (0.13), residues: 1708 sheet: 0.32 (0.25), residues: 428 loop : 0.89 (0.18), residues: 1356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 283 time to evaluate : 3.378 Fit side-chains outliers start: 57 outliers final: 41 residues processed: 323 average time/residue: 1.0787 time to fit residues: 429.2266 Evaluate side-chains 320 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 279 time to evaluate : 3.417 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 34 residues processed: 7 average time/residue: 0.7604 time to fit residues: 11.6353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 0.9980 chunk 207 optimal weight: 0.2980 chunk 334 optimal weight: 0.0020 chunk 204 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 350 optimal weight: 0.9990 chunk 322 optimal weight: 7.9990 chunk 279 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 215 optimal weight: 0.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 172 ASN C 372 HIS C 616 GLN D 372 HIS D 616 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 29536 Z= 0.129 Angle : 0.445 9.570 40002 Z= 0.220 Chirality : 0.039 0.277 4528 Planarity : 0.004 0.071 4946 Dihedral : 8.342 167.674 4234 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.15), residues: 3492 helix: 1.07 (0.13), residues: 1704 sheet: 0.30 (0.25), residues: 428 loop : 0.85 (0.18), residues: 1360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 288 time to evaluate : 3.634 Fit side-chains outliers start: 46 outliers final: 39 residues processed: 326 average time/residue: 1.1277 time to fit residues: 453.0445 Evaluate side-chains 320 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 281 time to evaluate : 3.345 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 34 residues processed: 5 average time/residue: 0.7290 time to fit residues: 9.2850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 257 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 279 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 287 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 172 ASN C 372 HIS C 616 GLN D 372 HIS D 616 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.078725 restraints weight = 38410.569| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.63 r_work: 0.2905 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work: 0.2872 rms_B_bonded: 2.38 restraints_weight: 0.1250 r_work: 0.2856 rms_B_bonded: 2.43 restraints_weight: 0.0625 r_work: 0.2839 rms_B_bonded: 2.52 restraints_weight: 0.0312 r_work: 0.2822 rms_B_bonded: 2.63 restraints_weight: 0.0156 r_work: 0.2804 rms_B_bonded: 2.77 restraints_weight: 0.0078 r_work: 0.2785 rms_B_bonded: 2.94 restraints_weight: 0.0039 r_work: 0.2766 rms_B_bonded: 3.14 restraints_weight: 0.0020 r_work: 0.2746 rms_B_bonded: 3.37 restraints_weight: 0.0010 r_work: 0.2725 rms_B_bonded: 3.64 restraints_weight: 0.0005 r_work: 0.2703 rms_B_bonded: 3.93 restraints_weight: 0.0002 r_work: 0.2680 rms_B_bonded: 4.27 restraints_weight: 0.0001 r_work: 0.2655 rms_B_bonded: 4.64 restraints_weight: 0.0001 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 29536 Z= 0.148 Angle : 0.451 8.815 40002 Z= 0.224 Chirality : 0.039 0.273 4528 Planarity : 0.004 0.067 4946 Dihedral : 8.234 166.927 4234 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3492 helix: 1.09 (0.13), residues: 1708 sheet: 0.32 (0.25), residues: 428 loop : 0.83 (0.18), residues: 1356 =============================================================================== Job complete usr+sys time: 8454.80 seconds wall clock time: 151 minutes 57.03 seconds (9117.03 seconds total)