Starting phenix.real_space_refine on Thu Mar 21 02:21:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/03_2024/7pxh_13703_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/03_2024/7pxh_13703.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/03_2024/7pxh_13703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/03_2024/7pxh_13703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/03_2024/7pxh_13703_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxh_13703/03_2024/7pxh_13703_updated.pdb" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 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. 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: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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, ' CA': 2, ' MG': 1, '6PL': 4, '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: {' CA': 2, ' MG': 1, '6PL': 4, '8I2': 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, ' CA': 2, ' MG': 1, '6PL': 4, '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: {' CA': 2, ' MG': 1, '6PL': 4, '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: 3.35, per 1000 atoms: 0.12 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: 14.97 Conformation dependent library (CDL) restraints added in 6.9 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: 7.17 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: 9.87 Time building geometry restraints manager: 16.04 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=" C11 6PL B1207 " pdb=" O3 6PL B1207 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C11 6PL D1206 " pdb=" O3 6PL D1206 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C11 6PL A1205 " pdb=" O3 6PL A1205 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C11 6PL B1205 " pdb=" O3 6PL B1205 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C11 6PL D1204 " pdb=" O3 6PL D1204 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.39e+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=" 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 angle pdb=" O3P 6PL C1206 " pdb=" P 6PL C1206 " pdb=" O4P 6PL C1206 " ideal model delta sigma weight residual 93.65 109.45 -15.80 3.00e+00 1.11e-01 2.77e+01 ... (remaining 39997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 16247 17.57 - 35.14: 1268 35.14 - 52.70: 295 52.70 - 70.27: 104 70.27 - 87.84: 22 Dihedral angle restraints: 17936 sinusoidal: 7596 harmonic: 10340 Sorted by residual: dihedral pdb=" CG ARG D1060 " pdb=" CD ARG D1060 " pdb=" NE ARG D1060 " pdb=" CZ ARG D1060 " ideal model delta sinusoidal sigma weight residual 180.00 -135.27 -44.73 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG C1060 " pdb=" CD ARG C1060 " pdb=" NE ARG C1060 " pdb=" CZ ARG C1060 " ideal model delta sinusoidal sigma weight residual 180.00 -135.28 -44.72 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA GLU A 969 " pdb=" C GLU A 969 " pdb=" N LEU A 970 " pdb=" CA LEU A 970 " ideal model delta harmonic sigma weight residual -180.00 -163.90 -16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 17933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4103 0.066 - 0.131: 391 0.131 - 0.197: 9 0.197 - 0.262: 20 0.262 - 0.328: 5 Chirality restraints: 4528 Sorted by residual: 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 chirality pdb=" C14 CLR A1208 " pdb=" C13 CLR A1208 " pdb=" C15 CLR A1208 " pdb=" C8 CLR A1208 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C14 CLR C1208 " pdb=" C13 CLR C1208 " pdb=" C15 CLR C1208 " pdb=" C8 CLR C1208 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.33 2.00e-01 2.50e+01 2.67e+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 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: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 35.250 Check model and map are aligned: 0.000 Set scattering table: 14.460 Process input model: 69.670 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 0.117 29536 Z= 0.363 Angle : 0.788 16.090 40002 Z= 0.314 Chirality : 0.042 0.328 4528 Planarity : 0.004 0.077 4946 Dihedral : 14.202 87.839 11240 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 % Allowed : 0.45 % Favored : 99.10 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 539 HIS 0.005 0.000 HIS D 372 PHE 0.007 0.001 PHE C 174 TYR 0.014 0.001 TYR B 197 ARG 0.006 0.000 ARG C 127 *********************** 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 : 3.264 Fit side-chains REVERT: A 255 SER cc_start: 0.9060 (m) cc_final: 0.8849 (m) REVERT: C 50 TRP cc_start: 0.8103 (p-90) cc_final: 0.7848 (p90) REVERT: D 571 LEU cc_start: 0.9206 (tt) cc_final: 0.8966 (tm) REVERT: D 1106 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7459 (ttp80) outliers start: 14 outliers final: 0 residues processed: 429 average time/residue: 1.1851 time to fit residues: 609.2877 Evaluate side-chains 321 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 3.082 ------------------------------------------------------------------------------- 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: 0.8488 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29536 Z= 0.231 Angle : 0.509 7.127 40002 Z= 0.259 Chirality : 0.041 0.292 4528 Planarity : 0.004 0.067 4946 Dihedral : 10.602 77.835 4724 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.07 % Allowed : 8.66 % Favored : 89.28 % 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: 0.90 (0.14), residues: 3492 helix: 0.75 (0.13), residues: 1664 sheet: 0.54 (0.24), residues: 468 loop : 0.68 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.005 0.001 HIS C 372 PHE 0.029 0.001 PHE B 134 TYR 0.014 0.001 TYR B1103 ARG 0.004 0.000 ARG D1064 *********************** 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 398 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 334 time to evaluate : 3.394 Fit side-chains REVERT: A 388 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: A 1097 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8808 (mtp) REVERT: B 388 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: B 1038 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7908 (mm-30) REVERT: C 122 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: C 191 TRP cc_start: 0.8205 (m100) cc_final: 0.7703 (m-90) REVERT: D 122 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7770 (mt0) REVERT: D 571 LEU cc_start: 0.9223 (tt) cc_final: 0.8983 (tm) REVERT: D 800 ASP cc_start: 0.7987 (m-30) cc_final: 0.7636 (m-30) REVERT: D 990 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7630 (mm-30) REVERT: D 1106 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7584 (ttp80) outliers start: 64 outliers final: 34 residues processed: 361 average time/residue: 1.1560 time to fit residues: 504.2780 Evaluate side-chains 351 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 312 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 1097 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 800 ASP Chi-restraints excluded: chain B residue 912 LYS Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain C residue 1034 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1034 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 266 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 4.9990 chunk 345 optimal weight: 0.0470 chunk 285 optimal weight: 0.0030 chunk 317 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 overall best weight: 1.1090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 372 HIS C 445 GLN D 445 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29536 Z= 0.194 Angle : 0.462 6.640 40002 Z= 0.234 Chirality : 0.040 0.287 4528 Planarity : 0.004 0.063 4946 Dihedral : 10.270 77.452 4724 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.87 % Allowed : 10.30 % Favored : 87.82 % 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: 1.00 (0.14), residues: 3492 helix: 0.81 (0.13), residues: 1668 sheet: 0.52 (0.25), residues: 420 loop : 0.78 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 114 HIS 0.006 0.001 HIS C 372 PHE 0.018 0.001 PHE A 134 TYR 0.017 0.001 TYR D 213 ARG 0.009 0.000 ARG C 829 *********************** 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 384 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 326 time to evaluate : 3.356 Fit side-chains REVERT: A 1038 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 1048 ARG cc_start: 0.8449 (ttm170) cc_final: 0.8157 (mtp180) REVERT: B 388 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: B 1038 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7890 (mm-30) REVERT: C 127 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6968 (ptm160) REVERT: D 113 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7081 (t70) REVERT: D 800 ASP cc_start: 0.8012 (m-30) cc_final: 0.7619 (m-30) REVERT: D 1106 ARG cc_start: 0.8351 (ttp80) cc_final: 0.7656 (ttp80) outliers start: 58 outliers final: 22 residues processed: 355 average time/residue: 1.1682 time to fit residues: 498.1681 Evaluate side-chains 330 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 305 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 912 LYS Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1034 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 7.9990 chunk 240 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 chunk 340 optimal weight: 0.5980 chunk 167 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 91 optimal weight: 30.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 29536 Z= 0.233 Angle : 0.472 9.061 40002 Z= 0.238 Chirality : 0.041 0.272 4528 Planarity : 0.004 0.062 4946 Dihedral : 10.032 76.544 4724 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.62 % Allowed : 10.40 % Favored : 86.98 % 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: 1.03 (0.14), residues: 3492 helix: 0.85 (0.13), residues: 1668 sheet: 0.43 (0.25), residues: 428 loop : 0.82 (0.18), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 191 HIS 0.006 0.001 HIS C 372 PHE 0.019 0.001 PHE A 525 TYR 0.012 0.001 TYR A1103 ARG 0.002 0.000 ARG C 285 *********************** 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 392 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 311 time to evaluate : 3.113 Fit side-chains REVERT: A 279 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8356 (t70) REVERT: A 1038 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 1048 ARG cc_start: 0.8450 (ttm170) cc_final: 0.8155 (mtp180) REVERT: B 285 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7991 (tpp-160) REVERT: B 388 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: B 1038 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7902 (mm-30) REVERT: C 550 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: D 113 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7073 (t70) REVERT: D 337 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7537 (mp) REVERT: D 550 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: D 551 MET cc_start: 0.8187 (tpp) cc_final: 0.7978 (mmm) outliers start: 81 outliers final: 36 residues processed: 352 average time/residue: 1.1279 time to fit residues: 480.1920 Evaluate side-chains 340 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 298 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 912 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1034 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 140 optimal weight: 0.0970 chunk 290 optimal weight: 0.3980 chunk 235 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 305 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 29536 Z= 0.148 Angle : 0.436 7.070 40002 Z= 0.221 Chirality : 0.039 0.282 4528 Planarity : 0.003 0.061 4946 Dihedral : 9.714 76.242 4724 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.26 % Allowed : 11.50 % Favored : 86.24 % 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: 1.09 (0.14), residues: 3492 helix: 0.95 (0.13), residues: 1668 sheet: 0.39 (0.25), residues: 420 loop : 0.80 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.006 0.001 HIS A 372 PHE 0.024 0.001 PHE B 134 TYR 0.014 0.001 TYR C 213 ARG 0.002 0.000 ARG D 829 *********************** 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 383 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 313 time to evaluate : 3.507 Fit side-chains REVERT: A 191 TRP cc_start: 0.7748 (m-90) cc_final: 0.6834 (m-90) REVERT: A 537 GLN cc_start: 0.7129 (mm-40) cc_final: 0.6737 (tp40) REVERT: A 1038 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 1048 ARG cc_start: 0.8442 (ttm170) cc_final: 0.8159 (mtp180) REVERT: B 285 ARG cc_start: 0.8219 (tpp-160) cc_final: 0.7948 (tpp-160) REVERT: B 537 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6628 (tp40) REVERT: B 912 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8457 (ttpp) REVERT: B 1048 ARG cc_start: 0.8450 (ttm170) cc_final: 0.8128 (mtp180) REVERT: C 191 TRP cc_start: 0.8212 (m100) cc_final: 0.7678 (m-90) REVERT: C 550 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: C 1038 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7685 (mt-10) REVERT: D 113 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7065 (t70) REVERT: D 413 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7057 (mm-30) REVERT: D 550 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7396 (pm20) outliers start: 70 outliers final: 33 residues processed: 347 average time/residue: 1.1357 time to fit residues: 475.6046 Evaluate side-chains 333 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 296 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 912 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 351 LYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 971 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 199 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 340 optimal weight: 0.8980 chunk 282 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2445 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= 0.155 Angle : 0.434 7.981 40002 Z= 0.219 Chirality : 0.039 0.275 4528 Planarity : 0.003 0.060 4946 Dihedral : 9.272 75.751 4724 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.16 % Allowed : 12.08 % Favored : 85.76 % 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 (0.14), residues: 3492 helix: 1.02 (0.13), residues: 1672 sheet: 0.37 (0.25), residues: 420 loop : 0.83 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.006 0.001 HIS A 372 PHE 0.015 0.001 PHE B 525 TYR 0.015 0.001 TYR C 213 ARG 0.002 0.000 ARG A 222 *********************** 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 370 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 303 time to evaluate : 3.288 Fit side-chains REVERT: A 191 TRP cc_start: 0.7717 (m-90) cc_final: 0.6788 (m-90) REVERT: A 388 GLU cc_start: 0.7641 (tt0) cc_final: 0.7296 (tm-30) REVERT: A 537 GLN cc_start: 0.7044 (mm-40) cc_final: 0.6733 (tp40) REVERT: A 1048 ARG cc_start: 0.8437 (ttm170) cc_final: 0.8160 (mtp180) REVERT: B 285 ARG cc_start: 0.8194 (tpp-160) cc_final: 0.7917 (tpp-160) REVERT: B 537 GLN cc_start: 0.6930 (mm-40) cc_final: 0.6619 (tp40) REVERT: B 912 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8446 (ttpp) REVERT: B 1048 ARG cc_start: 0.8455 (ttm170) cc_final: 0.8134 (mtp180) REVERT: C 337 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7426 (mp) REVERT: C 550 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: C 1038 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7682 (mt-10) REVERT: D 113 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7078 (t70) REVERT: D 337 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7394 (mp) REVERT: D 413 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7069 (mm-30) REVERT: D 550 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7750 (pt0) outliers start: 67 outliers final: 38 residues processed: 340 average time/residue: 1.1238 time to fit residues: 465.4150 Evaluate side-chains 338 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 294 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 912 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 802 ASN Chi-restraints excluded: chain D residue 971 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 286 optimal weight: 0.5980 chunk 190 optimal weight: 0.0470 chunk 339 optimal weight: 0.3980 chunk 212 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 445 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN D 372 HIS D 445 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2500 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= 0.126 Angle : 0.420 6.189 40002 Z= 0.213 Chirality : 0.039 0.277 4528 Planarity : 0.003 0.059 4946 Dihedral : 8.915 75.564 4724 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.78 % Allowed : 12.79 % Favored : 85.43 % 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: 1.24 (0.14), residues: 3492 helix: 1.11 (0.13), residues: 1664 sheet: 0.36 (0.25), residues: 420 loop : 0.87 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.005 0.001 HIS A 372 PHE 0.014 0.001 PHE D 174 TYR 0.015 0.001 TYR C 213 ARG 0.004 0.000 ARG D 829 *********************** 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 355 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 300 time to evaluate : 3.106 Fit side-chains REVERT: A 191 TRP cc_start: 0.7704 (m-90) cc_final: 0.6709 (m-90) REVERT: A 537 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6734 (tp40) REVERT: A 1048 ARG cc_start: 0.8435 (ttm170) cc_final: 0.8158 (mtp180) REVERT: B 191 TRP cc_start: 0.7746 (m-90) cc_final: 0.6864 (m-90) REVERT: B 537 GLN cc_start: 0.6923 (mm-40) cc_final: 0.6600 (tp40) REVERT: B 912 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8449 (ttpp) REVERT: B 1048 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8141 (mtp180) REVERT: C 413 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7052 (mm-30) REVERT: C 550 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: C 1038 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7667 (mt-10) REVERT: D 113 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7094 (t70) REVERT: D 122 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: D 413 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7058 (mm-30) REVERT: D 550 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7598 (pt0) outliers start: 55 outliers final: 37 residues processed: 331 average time/residue: 1.1479 time to fit residues: 463.9546 Evaluate side-chains 337 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 295 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 912 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 971 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 66 optimal weight: 0.0370 chunk 65 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 167 optimal weight: 0.0270 chunk 31 optimal weight: 0.5980 chunk 266 optimal weight: 5.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 372 HIS C 445 GLN D 122 GLN D 372 HIS D 445 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2522 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= 0.120 Angle : 0.414 6.445 40002 Z= 0.209 Chirality : 0.039 0.277 4528 Planarity : 0.003 0.059 4946 Dihedral : 8.772 75.493 4724 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.61 % Allowed : 12.95 % Favored : 85.43 % 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: 1.31 (0.14), residues: 3492 helix: 1.18 (0.13), residues: 1676 sheet: 0.37 (0.25), residues: 420 loop : 0.88 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.008 0.001 HIS A 372 PHE 0.016 0.001 PHE D 174 TYR 0.010 0.001 TYR A 856 ARG 0.002 0.000 ARG B1064 *********************** 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 350 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 300 time to evaluate : 3.183 Fit side-chains REVERT: A 191 TRP cc_start: 0.7708 (m-90) cc_final: 0.6693 (m-90) REVERT: A 388 GLU cc_start: 0.7742 (tt0) cc_final: 0.7414 (tm-30) REVERT: A 537 GLN cc_start: 0.6996 (mm-40) cc_final: 0.6741 (tp40) REVERT: A 1048 ARG cc_start: 0.8435 (ttm170) cc_final: 0.8158 (mtp180) REVERT: B 191 TRP cc_start: 0.7734 (m-90) cc_final: 0.6829 (m-90) REVERT: B 537 GLN cc_start: 0.6857 (mm-40) cc_final: 0.6591 (tp40) REVERT: B 1048 ARG cc_start: 0.8456 (ttm170) cc_final: 0.8150 (mtp180) REVERT: C 413 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7048 (mm-30) REVERT: C 550 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: C 1038 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7656 (mt-10) REVERT: D 113 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7061 (t70) REVERT: D 413 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7062 (mm-30) REVERT: D 550 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7587 (pt0) outliers start: 50 outliers final: 39 residues processed: 331 average time/residue: 1.0868 time to fit residues: 438.5897 Evaluate side-chains 336 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 294 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 802 ASN Chi-restraints excluded: chain D residue 971 VAL 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: 0.7980 chunk 296 optimal weight: 0.6980 chunk 316 optimal weight: 0.0670 chunk 324 optimal weight: 0.8980 chunk 190 optimal weight: 0.3980 chunk 137 optimal weight: 0.0030 chunk 248 optimal weight: 0.0470 chunk 97 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 overall best weight: 0.2426 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2570 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= 0.107 Angle : 0.409 6.565 40002 Z= 0.207 Chirality : 0.038 0.278 4528 Planarity : 0.003 0.059 4946 Dihedral : 8.508 75.321 4724 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.32 % Allowed : 13.50 % Favored : 85.17 % 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: 1.39 (0.15), residues: 3492 helix: 1.25 (0.13), residues: 1676 sheet: 0.40 (0.25), residues: 428 loop : 0.91 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 191 HIS 0.007 0.001 HIS A 372 PHE 0.017 0.001 PHE D 174 TYR 0.016 0.001 TYR D 213 ARG 0.002 0.000 ARG B1064 *********************** 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 349 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 308 time to evaluate : 3.183 Fit side-chains REVERT: A 191 TRP cc_start: 0.7669 (m-90) cc_final: 0.6688 (m-90) REVERT: A 388 GLU cc_start: 0.7727 (tt0) cc_final: 0.7434 (tm-30) REVERT: A 537 GLN cc_start: 0.6986 (mm-40) cc_final: 0.6705 (tp40) REVERT: A 1048 ARG cc_start: 0.8438 (ttm170) cc_final: 0.8170 (mtp180) REVERT: B 191 TRP cc_start: 0.7700 (m-90) cc_final: 0.6790 (m-90) REVERT: B 537 GLN cc_start: 0.6848 (mm-40) cc_final: 0.6626 (tp40) REVERT: B 1048 ARG cc_start: 0.8454 (ttm170) cc_final: 0.8157 (mtp180) REVERT: C 413 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7085 (mm-30) REVERT: C 550 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: C 1038 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7636 (mt-10) REVERT: D 413 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7044 (mm-30) REVERT: D 550 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7262 (pm20) outliers start: 41 outliers final: 32 residues processed: 335 average time/residue: 1.1217 time to fit residues: 459.7278 Evaluate side-chains 329 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 295 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 971 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 334 optimal weight: 0.0050 chunk 204 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 350 optimal weight: 0.9990 chunk 322 optimal weight: 0.8980 chunk 279 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 D 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2619 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= 0.146 Angle : 0.422 7.506 40002 Z= 0.213 Chirality : 0.039 0.279 4528 Planarity : 0.003 0.058 4946 Dihedral : 8.382 74.954 4724 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.45 % Allowed : 13.60 % Favored : 84.95 % 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: 1.39 (0.14), residues: 3492 helix: 1.27 (0.13), residues: 1676 sheet: 0.42 (0.25), residues: 420 loop : 0.88 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 191 HIS 0.008 0.001 HIS B 372 PHE 0.027 0.001 PHE C 174 TYR 0.014 0.001 TYR C 213 ARG 0.002 0.000 ARG C 545 ********************** 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 341 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 296 time to evaluate : 3.334 Fit side-chains REVERT: A 388 GLU cc_start: 0.7741 (tt0) cc_final: 0.7442 (tm-30) REVERT: A 537 GLN cc_start: 0.7024 (mm-40) cc_final: 0.6810 (tp40) REVERT: A 1048 ARG cc_start: 0.8440 (ttm170) cc_final: 0.8163 (mtp180) REVERT: B 191 TRP cc_start: 0.7707 (m-90) cc_final: 0.6769 (m-90) REVERT: B 537 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6633 (tp40) REVERT: B 1048 ARG cc_start: 0.8436 (ttm170) cc_final: 0.8135 (mtp180) REVERT: C 191 TRP cc_start: 0.8243 (m100) cc_final: 0.7746 (m-90) REVERT: C 413 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7055 (mm-30) REVERT: C 550 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: C 862 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.7738 (tmmm) REVERT: C 1038 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7667 (mt-10) REVERT: D 413 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7057 (mm-30) REVERT: D 550 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7258 (pm20) outliers start: 45 outliers final: 36 residues processed: 325 average time/residue: 1.1191 time to fit residues: 441.1046 Evaluate side-chains 329 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 290 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 862 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 971 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 85 optimal weight: 0.0050 chunk 257 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 279 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 287 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 372 HIS D 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.080123 restraints weight = 38598.422| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.60 r_work: 0.2778 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2653 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= 0.139 Angle : 0.421 6.784 40002 Z= 0.213 Chirality : 0.039 0.279 4528 Planarity : 0.003 0.059 4946 Dihedral : 8.273 74.852 4724 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.36 % Allowed : 13.66 % Favored : 84.98 % 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: 1.31 (0.15), residues: 3492 helix: 1.20 (0.13), residues: 1700 sheet: 0.42 (0.25), residues: 420 loop : 0.84 (0.18), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 191 HIS 0.009 0.001 HIS B 372 PHE 0.019 0.001 PHE C 174 TYR 0.017 0.001 TYR D 213 ARG 0.001 0.000 ARG A 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9681.96 seconds wall clock time: 173 minutes 13.01 seconds (10393.01 seconds total)