Starting phenix.real_space_refine on Thu Mar 21 20:53:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5weo_8823/03_2024/5weo_8823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5weo_8823/03_2024/5weo_8823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5weo_8823/03_2024/5weo_8823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5weo_8823/03_2024/5weo_8823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5weo_8823/03_2024/5weo_8823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5weo_8823/03_2024/5weo_8823_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 172 5.16 5 Cl 4 4.86 5 C 20049 2.51 5 N 5139 2.21 5 O 5804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 1005": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D ARG 309": "NH1" <-> "NH2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 1005": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31168 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7765 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 962} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 7753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7753 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 961} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 7765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7765 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 962} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 7749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7749 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 961} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Time building chain proxies: 16.20, per 1000 atoms: 0.52 Number of scatterers: 31168 At special positions: 0 Unit cell: (115.56, 169.56, 199.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 172 16.00 O 5804 8.00 N 5139 7.00 C 20049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.37 Conformation dependent library (CDL) restraints added in 5.8 seconds 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 130 helices and 32 sheets defined 43.4% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.33 Creating SS restraints... Processing helix chain 'A' and resid 23 through 36 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 82 through 92 removed outlier: 4.078A pdb=" N THR A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.625A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.660A pdb=" N GLN A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 removed outlier: 4.196A pdb=" N ASP A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.769A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.747A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.656A pdb=" N MET A 527 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.850A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 623 removed outlier: 3.648A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 641 No H-bonds generated for 'chain 'A' and resid 638 through 641' Processing helix chain 'A' and resid 654 through 661 removed outlier: 3.795A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.849A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 790 through 819 removed outlier: 5.803A pdb=" N GLY A 794 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 795 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 800 " --> pdb=" O TYR A 797 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 801 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 804 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 810 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 813 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS A 815 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 819 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1027 removed outlier: 3.816A pdb=" N THR A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1101 Processing helix chain 'A' and resid 1105 through 1124 removed outlier: 3.799A pdb=" N LEU A1114 " --> pdb=" O SER A1110 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A1122 " --> pdb=" O GLY A1118 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A1124 " --> pdb=" O CYS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1160 removed outlier: 3.863A pdb=" N GLY A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A1141 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1208 removed outlier: 3.842A pdb=" N GLY A1182 " --> pdb=" O PHE A1179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A1185 " --> pdb=" O GLY A1182 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A1189 " --> pdb=" O PHE A1186 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A1192 " --> pdb=" O ALA A1189 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A1193 " --> pdb=" O GLU A1190 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A1194 " --> pdb=" O MET A1191 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A1202 " --> pdb=" O MET A1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 36 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 82 through 92 removed outlier: 4.078A pdb=" N THR B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.625A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.661A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 211 removed outlier: 4.197A pdb=" N ASP B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.769A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 333 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 436 removed outlier: 3.747A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 468 Processing helix chain 'B' and resid 514 through 520 removed outlier: 4.505A pdb=" N PHE B 517 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 523 through 543 removed outlier: 3.569A pdb=" N GLY B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 599 through 616 removed outlier: 3.742A pdb=" N GLY B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 641 No H-bonds generated for 'chain 'B' and resid 638 through 641' Processing helix chain 'B' and resid 654 through 661 removed outlier: 3.795A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.850A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 774 through 780 removed outlier: 3.971A pdb=" N SER B 778 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY B 779 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 793 through 816 removed outlier: 3.586A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 803 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 804 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 813 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1027 removed outlier: 3.816A pdb=" N THR B1013 " --> pdb=" O MET B1009 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B1014 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B1024 " --> pdb=" O PHE B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1101 Processing helix chain 'B' and resid 1105 through 1124 removed outlier: 3.800A pdb=" N LEU B1114 " --> pdb=" O SER B1110 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA B1122 " --> pdb=" O GLY B1118 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B1123 " --> pdb=" O LEU B1119 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B1124 " --> pdb=" O CYS B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1160 removed outlier: 3.864A pdb=" N GLY B1138 " --> pdb=" O ILE B1134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B1139 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B1160 " --> pdb=" O ILE B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1208 removed outlier: 3.842A pdb=" N GLY B1182 " --> pdb=" O PHE B1179 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B1185 " --> pdb=" O GLY B1182 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B1189 " --> pdb=" O PHE B1186 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B1192 " --> pdb=" O ALA B1189 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B1193 " --> pdb=" O GLU B1190 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B1194 " --> pdb=" O MET B1191 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP B1202 " --> pdb=" O MET B1199 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 82 through 92 removed outlier: 4.078A pdb=" N THR C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.625A pdb=" N LEU C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.662A pdb=" N GLN C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 211 removed outlier: 4.196A pdb=" N ASP C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.770A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 333 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.746A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 Processing helix chain 'C' and resid 523 through 544 removed outlier: 3.656A pdb=" N MET C 527 " --> pdb=" O TYR C 523 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.849A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 623 removed outlier: 3.649A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 641 No H-bonds generated for 'chain 'C' and resid 638 through 641' Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.796A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 676 Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.849A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 790 through 819 removed outlier: 5.803A pdb=" N GLY C 794 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 795 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 800 " --> pdb=" O TYR C 797 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY C 801 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 804 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA C 810 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 813 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS C 815 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 819 " --> pdb=" O TYR C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1027 removed outlier: 3.816A pdb=" N THR C1013 " --> pdb=" O MET C1009 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C1014 " --> pdb=" O LEU C1010 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR C1024 " --> pdb=" O PHE C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1092 through 1101 Processing helix chain 'C' and resid 1105 through 1124 removed outlier: 3.799A pdb=" N LEU C1114 " --> pdb=" O SER C1110 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C1123 " --> pdb=" O LEU C1119 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER C1124 " --> pdb=" O CYS C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1160 removed outlier: 3.864A pdb=" N GLY C1138 " --> pdb=" O ILE C1134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C1139 " --> pdb=" O LEU C1135 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C1141 " --> pdb=" O ALA C1137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C1160 " --> pdb=" O ILE C1156 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1208 removed outlier: 3.842A pdb=" N GLY C1182 " --> pdb=" O PHE C1179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C1185 " --> pdb=" O GLY C1182 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C1189 " --> pdb=" O PHE C1186 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL C1192 " --> pdb=" O ALA C1189 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C1193 " --> pdb=" O GLU C1190 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL C1194 " --> pdb=" O MET C1191 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP C1202 " --> pdb=" O MET C1199 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 82 through 92 removed outlier: 4.078A pdb=" N THR D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.625A pdb=" N LEU D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 175 through 187 removed outlier: 3.661A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 removed outlier: 4.196A pdb=" N ASP D 206 " --> pdb=" O ASN D 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.770A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 333 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.747A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 514 through 520 removed outlier: 4.504A pdb=" N PHE D 517 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 523 through 543 removed outlier: 3.569A pdb=" N GLY D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 599 through 616 removed outlier: 3.743A pdb=" N GLY D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 641 No H-bonds generated for 'chain 'D' and resid 638 through 641' Processing helix chain 'D' and resid 654 through 661 removed outlier: 3.796A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.849A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 753 " --> pdb=" O ALA D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 774 through 780 removed outlier: 3.971A pdb=" N SER D 778 " --> pdb=" O ALA D 775 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY D 779 " --> pdb=" O LYS D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 793 through 816 removed outlier: 3.586A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 803 " --> pdb=" O LEU D 799 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D 804 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 812 " --> pdb=" O LEU D 808 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 813 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS D 815 " --> pdb=" O LEU D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 1007 through 1027 removed outlier: 3.816A pdb=" N THR D1013 " --> pdb=" O MET D1009 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D1014 " --> pdb=" O LEU D1010 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D1024 " --> pdb=" O PHE D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1092 through 1101 Processing helix chain 'D' and resid 1105 through 1124 removed outlier: 3.800A pdb=" N LEU D1114 " --> pdb=" O SER D1110 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA D1122 " --> pdb=" O GLY D1118 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D1123 " --> pdb=" O LEU D1119 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D1124 " --> pdb=" O CYS D1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1160 removed outlier: 3.863A pdb=" N GLY D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D1139 " --> pdb=" O LEU D1135 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY D1151 " --> pdb=" O SER D1147 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D1160 " --> pdb=" O ILE D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1208 removed outlier: 3.842A pdb=" N GLY D1182 " --> pdb=" O PHE D1179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D1185 " --> pdb=" O GLY D1182 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D1189 " --> pdb=" O PHE D1186 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL D1192 " --> pdb=" O ALA D1189 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D1193 " --> pdb=" O GLU D1190 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL D1194 " --> pdb=" O MET D1191 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D1202 " --> pdb=" O MET D1199 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 49 removed outlier: 3.604A pdb=" N HIS A 46 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA A 72 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU A 17 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE A 74 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.412A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 394 through 399 removed outlier: 7.179A pdb=" N LYS A 439 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL A 397 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 441 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR A 399 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 443 " --> pdb=" O THR A 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= F, first strand: chain 'A' and resid 720 through 722 removed outlier: 6.253A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 3.537A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A1066 " --> pdb=" O HIS A1059 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.788A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 42 through 49 removed outlier: 3.604A pdb=" N HIS B 46 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA B 72 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU B 17 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE B 74 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= K, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.413A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 394 through 399 removed outlier: 7.281A pdb=" N LYS B 439 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL B 397 " --> pdb=" O LYS B 439 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS B 441 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR B 399 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR B 443 " --> pdb=" O THR B 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= N, first strand: chain 'B' and resid 720 through 722 removed outlier: 6.253A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 1033 through 1037 removed outlier: 3.537A pdb=" N SER B1035 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS B1066 " --> pdb=" O HIS B1059 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 494 through 498 removed outlier: 6.789A pdb=" N TYR B 732 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B 497 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS B 730 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 42 through 49 removed outlier: 3.603A pdb=" N HIS C 46 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 72 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU C 17 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE C 74 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= S, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.413A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 394 through 399 removed outlier: 7.204A pdb=" N LYS C 439 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL C 397 " --> pdb=" O LYS C 439 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS C 441 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR C 399 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR C 443 " --> pdb=" O THR C 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= V, first strand: chain 'C' and resid 720 through 722 removed outlier: 6.253A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 1033 through 1037 removed outlier: 3.537A pdb=" N SER C1035 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS C1066 " --> pdb=" O HIS C1059 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.788A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 42 through 49 removed outlier: 3.604A pdb=" N HIS D 46 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA D 72 " --> pdb=" O GLY D 15 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU D 17 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE D 74 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 96 through 98 Processing sheet with id= AA, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.411A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 394 through 399 removed outlier: 7.043A pdb=" N LYS D 439 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL D 397 " --> pdb=" O LYS D 439 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS D 441 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR D 399 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR D 443 " --> pdb=" O THR D 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= AD, first strand: chain 'D' and resid 720 through 722 removed outlier: 6.253A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 1033 through 1037 removed outlier: 3.537A pdb=" N SER D1035 " --> pdb=" O THR D1058 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS D1066 " --> pdb=" O HIS D1059 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 494 through 498 removed outlier: 6.788A pdb=" N TYR D 732 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER D 497 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS D 730 " --> pdb=" O SER D 497 " (cutoff:3.500A) 1154 hydrogen bonds defined for protein. 3048 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: 12.05 Time building geometry restraints manager: 14.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 5083 1.27 - 1.41: 8151 1.41 - 1.55: 18308 1.55 - 1.69: 18 1.69 - 1.83: 280 Bond restraints: 31840 Sorted by residual: bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.125 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.125 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.126 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.126 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C1 CYZ A1302 " pdb=" C6 CYZ A1302 " ideal model delta sigma weight residual 1.553 1.755 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 31835 not shown) Histogram of bond angle deviations from ideal: 93.12 - 101.32: 117 101.32 - 109.53: 4107 109.53 - 117.74: 19516 117.74 - 125.95: 18838 125.95 - 134.16: 456 Bond angle restraints: 43034 Sorted by residual: angle pdb=" N GLU B 384 " pdb=" CA GLU B 384 " pdb=" C GLU B 384 " ideal model delta sigma weight residual 110.91 120.45 -9.54 1.17e+00 7.31e-01 6.65e+01 angle pdb=" N GLU D 384 " pdb=" CA GLU D 384 " pdb=" C GLU D 384 " ideal model delta sigma weight residual 110.91 120.44 -9.53 1.17e+00 7.31e-01 6.63e+01 angle pdb=" O3 CYZ C1302 " pdb=" S2 CYZ C1302 " pdb=" O4 CYZ C1302 " ideal model delta sigma weight residual 118.35 100.34 18.01 3.00e+00 1.11e-01 3.61e+01 angle pdb=" O3 CYZ A1302 " pdb=" S2 CYZ A1302 " pdb=" O4 CYZ A1302 " ideal model delta sigma weight residual 118.35 101.23 17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O3 CYZ B1302 " pdb=" S2 CYZ B1302 " pdb=" O4 CYZ B1302 " ideal model delta sigma weight residual 118.35 101.31 17.04 3.00e+00 1.11e-01 3.22e+01 ... (remaining 43029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.17: 18592 27.17 - 54.33: 252 54.33 - 81.50: 14 81.50 - 108.66: 8 108.66 - 135.83: 8 Dihedral angle restraints: 18874 sinusoidal: 7516 harmonic: 11358 Sorted by residual: dihedral pdb=" CA SER D 635 " pdb=" C SER D 635 " pdb=" N ALA D 636 " pdb=" CA ALA D 636 " ideal model delta harmonic sigma weight residual -180.00 -126.33 -53.67 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA SER B 635 " pdb=" C SER B 635 " pdb=" N ALA B 636 " pdb=" CA ALA B 636 " ideal model delta harmonic sigma weight residual -180.00 -126.33 -53.67 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA SER C 635 " pdb=" C SER C 635 " pdb=" N ALA C 636 " pdb=" CA ALA C 636 " ideal model delta harmonic sigma weight residual 180.00 -126.34 -53.66 0 5.00e+00 4.00e-02 1.15e+02 ... (remaining 18871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 4691 0.146 - 0.293: 75 0.293 - 0.439: 0 0.439 - 0.585: 0 0.585 - 0.731: 8 Chirality restraints: 4774 Sorted by residual: chirality pdb=" C2 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" C3 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 2.58 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C2 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" C3 CYZ D1302 " pdb=" C7 CYZ D1302 " both_signs ideal model delta sigma weight residual False 3.31 2.58 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.58 0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 4771 not shown) Planarity restraints: 5408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.060 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO D 99 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.060 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO A 99 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.060 5.00e-02 4.00e+02 9.18e-02 1.35e+01 pdb=" N PRO B 99 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.049 5.00e-02 4.00e+02 ... (remaining 5405 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2826 2.73 - 3.27: 32566 3.27 - 3.82: 53827 3.82 - 4.36: 63997 4.36 - 4.90: 99489 Nonbonded interactions: 252705 Sorted by model distance: nonbonded pdb=" OG SER A 87 " pdb=" OD1 ASN B 54 " model vdw 2.188 2.440 nonbonded pdb=" O TYR A1031 " pdb=" OG SER A1178 " model vdw 2.218 2.440 nonbonded pdb=" O TYR D1031 " pdb=" OG SER D1178 " model vdw 2.219 2.440 nonbonded pdb=" O TYR C1031 " pdb=" OG SER C1178 " model vdw 2.219 2.440 nonbonded pdb=" O TYR B1031 " pdb=" OG SER B1178 " model vdw 2.219 2.440 ... (remaining 252700 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 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1002 through 12 \ 09 or resid 1301 through 1302)) selection = (chain 'B' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 1209 or resid 1301 through 1302 \ )) selection = (chain 'C' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1002 through 12 \ 09 or resid 1301 through 1302)) 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 7.630 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 84.710 Find NCS groups from input model: 2.360 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:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 : 0.009 0.209 31840 Z= 0.604 Angle : 1.053 18.015 43034 Z= 0.581 Chirality : 0.061 0.731 4774 Planarity : 0.007 0.092 5408 Dihedral : 10.707 135.829 11574 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.26 % Favored : 92.69 % Rotamer: Outliers : 0.24 % Allowed : 2.43 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.69 (0.11), residues: 3910 helix: -2.75 (0.09), residues: 1620 sheet: -2.45 (0.26), residues: 408 loop : -2.04 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 130 HIS 0.014 0.005 HIS C 214 PHE 0.027 0.003 PHE B1072 TYR 0.028 0.003 TYR A 218 ARG 0.011 0.001 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 766 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASP cc_start: 0.9275 (m-30) cc_final: 0.8754 (t70) REVERT: A 182 GLN cc_start: 0.8632 (mt0) cc_final: 0.8232 (tp40) REVERT: A 331 ARG cc_start: 0.9118 (ttt-90) cc_final: 0.8916 (ptm160) REVERT: A 369 ARG cc_start: 0.7814 (ptm160) cc_final: 0.7523 (ttm-80) REVERT: A 427 ASP cc_start: 0.8518 (m-30) cc_final: 0.8309 (m-30) REVERT: A 527 MET cc_start: 0.8880 (ttt) cc_final: 0.8355 (tpt) REVERT: A 651 ASP cc_start: 0.7216 (m-30) cc_final: 0.6534 (m-30) REVERT: A 1022 LEU cc_start: 0.8118 (mt) cc_final: 0.7835 (tp) REVERT: A 1082 PHE cc_start: 0.7693 (p90) cc_final: 0.6204 (t80) REVERT: B 18 PHE cc_start: 0.8968 (m-80) cc_final: 0.8514 (m-80) REVERT: B 73 ILE cc_start: 0.8825 (mt) cc_final: 0.8152 (mt) REVERT: B 113 MET cc_start: 0.8074 (mmp) cc_final: 0.7526 (mpp) REVERT: B 159 GLN cc_start: 0.7958 (mt0) cc_final: 0.7723 (mp10) REVERT: B 167 ASN cc_start: 0.7917 (m-40) cc_final: 0.7691 (p0) REVERT: B 408 MET cc_start: 0.8990 (mmm) cc_final: 0.8692 (mmm) REVERT: B 414 MET cc_start: 0.8183 (mtm) cc_final: 0.7782 (ptp) REVERT: B 415 LEU cc_start: 0.6486 (mt) cc_final: 0.5540 (mm) REVERT: B 549 TYR cc_start: 0.7766 (p90) cc_final: 0.7418 (p90) REVERT: B 813 GLU cc_start: 0.8582 (tt0) cc_final: 0.8078 (mm-30) REVERT: B 814 PHE cc_start: 0.8676 (t80) cc_final: 0.8380 (t80) REVERT: B 1027 VAL cc_start: 0.8776 (t) cc_final: 0.8381 (m) REVERT: B 1064 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.7369 (mmt180) REVERT: B 1202 ASP cc_start: 0.8838 (m-30) cc_final: 0.8073 (t0) REVERT: C 171 ASP cc_start: 0.9163 (m-30) cc_final: 0.8757 (t0) REVERT: C 187 LYS cc_start: 0.9070 (mttt) cc_final: 0.8793 (mtmm) REVERT: C 304 ILE cc_start: 0.8613 (mt) cc_final: 0.7872 (tt) REVERT: C 369 ARG cc_start: 0.7414 (ptm160) cc_final: 0.7078 (ttm-80) REVERT: C 414 MET cc_start: 0.8488 (mtm) cc_final: 0.8215 (tpp) REVERT: C 527 MET cc_start: 0.8634 (ttt) cc_final: 0.8260 (tpt) REVERT: C 570 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8504 (mp0) REVERT: C 1009 MET cc_start: 0.8235 (tpt) cc_final: 0.7805 (mtp) REVERT: C 1022 LEU cc_start: 0.7987 (mt) cc_final: 0.7754 (tp) REVERT: D 18 PHE cc_start: 0.9012 (m-80) cc_final: 0.8734 (m-80) REVERT: D 73 ILE cc_start: 0.8957 (mt) cc_final: 0.8262 (mt) REVERT: D 113 MET cc_start: 0.8378 (mmp) cc_final: 0.7986 (mpp) REVERT: D 159 GLN cc_start: 0.8342 (mt0) cc_final: 0.7915 (mp10) REVERT: D 265 LEU cc_start: 0.6326 (mt) cc_final: 0.6004 (mt) REVERT: D 519 ASP cc_start: 0.8129 (t0) cc_final: 0.7706 (t70) REVERT: D 541 PHE cc_start: 0.9368 (t80) cc_final: 0.9028 (t80) REVERT: D 573 ILE cc_start: 0.8981 (tp) cc_final: 0.8639 (tp) REVERT: D 670 MET cc_start: 0.9155 (mtp) cc_final: 0.8951 (mmm) REVERT: D 797 TYR cc_start: 0.8680 (m-10) cc_final: 0.8460 (m-10) REVERT: D 813 GLU cc_start: 0.8921 (tt0) cc_final: 0.8293 (tm-30) REVERT: D 1022 LEU cc_start: 0.8395 (mt) cc_final: 0.8128 (tp) REVERT: D 1027 VAL cc_start: 0.8115 (t) cc_final: 0.7313 (m) REVERT: D 1202 ASP cc_start: 0.8893 (m-30) cc_final: 0.8241 (t0) outliers start: 8 outliers final: 0 residues processed: 769 average time/residue: 0.4581 time to fit residues: 539.3052 Evaluate side-chains 364 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.0370 chunk 297 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 307 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 355 optimal weight: 0.9980 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 355 ASN A1131 HIS A1132 ASN A1204 HIS B 24 GLN B 298 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN B 355 ASN B 412 HIS B 569 ASN B 586 GLN B1131 HIS B1132 ASN B1204 HIS C 337 GLN C 350 ASN C 355 ASN C 587 GLN C 726 ASN C1131 HIS C1132 ASN D 24 GLN D 298 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 355 ASN D 412 HIS D 569 ASN D 586 GLN D1131 HIS D1132 ASN D1159 ASN D1204 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31840 Z= 0.175 Angle : 0.570 7.310 43034 Z= 0.308 Chirality : 0.041 0.235 4774 Planarity : 0.005 0.070 5408 Dihedral : 7.830 98.266 4388 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.88 (0.12), residues: 3910 helix: -0.54 (0.11), residues: 1716 sheet: -1.78 (0.29), residues: 364 loop : -1.78 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1032 HIS 0.013 0.002 HIS D1059 PHE 0.018 0.001 PHE B 541 TYR 0.025 0.001 TYR D 523 ARG 0.008 0.001 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 467 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8064 (mmm) cc_final: 0.7663 (mmm) REVERT: A 182 GLN cc_start: 0.8828 (mt0) cc_final: 0.8370 (tp40) REVERT: A 369 ARG cc_start: 0.7721 (ptm160) cc_final: 0.7457 (mtp85) REVERT: A 382 LEU cc_start: 0.9028 (pp) cc_final: 0.8758 (tp) REVERT: A 431 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8622 (mm-30) REVERT: A 450 TYR cc_start: 0.8446 (m-80) cc_final: 0.8241 (m-80) REVERT: A 527 MET cc_start: 0.8736 (ttt) cc_final: 0.8300 (tpt) REVERT: A 670 MET cc_start: 0.9078 (mtp) cc_final: 0.8721 (mtt) REVERT: A 1082 PHE cc_start: 0.7623 (p90) cc_final: 0.5993 (t80) REVERT: A 1191 MET cc_start: 0.8846 (mtp) cc_final: 0.8533 (mtp) REVERT: B 73 ILE cc_start: 0.8741 (mt) cc_final: 0.8110 (mt) REVERT: B 126 GLU cc_start: 0.9390 (mt-10) cc_final: 0.8956 (mp0) REVERT: B 407 MET cc_start: 0.8811 (mtm) cc_final: 0.8536 (mtt) REVERT: B 408 MET cc_start: 0.9209 (mmm) cc_final: 0.8995 (mmm) REVERT: B 414 MET cc_start: 0.8449 (mtm) cc_final: 0.7999 (ptp) REVERT: B 503 MET cc_start: 0.6887 (tmm) cc_final: 0.6590 (tmm) REVERT: B 519 ASP cc_start: 0.8176 (t0) cc_final: 0.7838 (t70) REVERT: B 527 MET cc_start: 0.7425 (tpp) cc_final: 0.7176 (tpp) REVERT: B 576 SER cc_start: 0.8605 (t) cc_final: 0.8397 (t) REVERT: B 604 VAL cc_start: 0.8867 (t) cc_final: 0.8656 (p) REVERT: B 729 SER cc_start: 0.8270 (m) cc_final: 0.7720 (t) REVERT: B 813 GLU cc_start: 0.8641 (tt0) cc_final: 0.8093 (mm-30) REVERT: B 814 PHE cc_start: 0.8737 (t80) cc_final: 0.8450 (t80) REVERT: B 1022 LEU cc_start: 0.8657 (tp) cc_final: 0.8426 (tp) REVERT: B 1027 VAL cc_start: 0.8467 (t) cc_final: 0.8139 (p) REVERT: B 1191 MET cc_start: 0.8839 (tpp) cc_final: 0.8589 (tpp) REVERT: B 1202 ASP cc_start: 0.8854 (m-30) cc_final: 0.8179 (t0) REVERT: C 171 ASP cc_start: 0.9120 (m-30) cc_final: 0.8827 (t0) REVERT: C 431 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8782 (mm-30) REVERT: C 519 ASP cc_start: 0.8752 (t0) cc_final: 0.8544 (t0) REVERT: C 527 MET cc_start: 0.8580 (ttt) cc_final: 0.8348 (tpt) REVERT: C 596 LEU cc_start: 0.8915 (tt) cc_final: 0.8641 (tt) REVERT: C 600 ILE cc_start: 0.9100 (tp) cc_final: 0.8764 (pt) REVERT: C 670 MET cc_start: 0.9097 (mtp) cc_final: 0.8756 (mtt) REVERT: C 1009 MET cc_start: 0.8621 (tpt) cc_final: 0.8319 (mtt) REVERT: C 1069 GLU cc_start: 0.7881 (tp30) cc_final: 0.7607 (tp30) REVERT: C 1091 ASP cc_start: 0.8118 (m-30) cc_final: 0.7891 (m-30) REVERT: C 1186 PHE cc_start: 0.8815 (t80) cc_final: 0.8296 (t80) REVERT: C 1188 ILE cc_start: 0.9345 (mt) cc_final: 0.9107 (tp) REVERT: D 73 ILE cc_start: 0.8895 (mt) cc_final: 0.8308 (mt) REVERT: D 126 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9000 (mp0) REVERT: D 159 GLN cc_start: 0.7973 (mt0) cc_final: 0.7591 (mp10) REVERT: D 262 TRP cc_start: 0.7530 (t-100) cc_final: 0.7300 (t-100) REVERT: D 358 ILE cc_start: 0.8579 (mm) cc_final: 0.8131 (mm) REVERT: D 360 ILE cc_start: 0.8719 (mm) cc_final: 0.8480 (mm) REVERT: D 414 MET cc_start: 0.8284 (mtm) cc_final: 0.7950 (ptp) REVERT: D 503 MET cc_start: 0.7560 (tmm) cc_final: 0.7168 (tmm) REVERT: D 519 ASP cc_start: 0.8379 (t0) cc_final: 0.8122 (t70) REVERT: D 527 MET cc_start: 0.7833 (tpp) cc_final: 0.7597 (tpp) REVERT: D 580 SER cc_start: 0.9033 (m) cc_final: 0.8810 (p) REVERT: D 670 MET cc_start: 0.9115 (mtp) cc_final: 0.8689 (mmm) REVERT: D 721 MET cc_start: 0.6954 (mmm) cc_final: 0.6599 (mmm) REVERT: D 797 TYR cc_start: 0.8820 (m-10) cc_final: 0.8542 (m-10) REVERT: D 814 PHE cc_start: 0.8789 (t80) cc_final: 0.8567 (t80) REVERT: D 1027 VAL cc_start: 0.7939 (t) cc_final: 0.7073 (p) REVERT: D 1202 ASP cc_start: 0.8903 (m-30) cc_final: 0.8399 (t0) outliers start: 3 outliers final: 0 residues processed: 470 average time/residue: 0.4086 time to fit residues: 309.4984 Evaluate side-chains 294 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.0970 chunk 110 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 242 optimal weight: 0.0370 chunk 98 optimal weight: 10.0000 chunk 356 optimal weight: 9.9990 chunk 385 optimal weight: 8.9990 chunk 317 optimal weight: 1.9990 chunk 353 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 overall best weight: 1.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS C 46 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN C 726 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31840 Z= 0.207 Angle : 0.556 8.927 43034 Z= 0.295 Chirality : 0.040 0.167 4774 Planarity : 0.005 0.077 5408 Dihedral : 6.695 80.885 4388 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.13), residues: 3910 helix: 0.49 (0.12), residues: 1754 sheet: -1.63 (0.28), residues: 358 loop : -1.62 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C1032 HIS 0.007 0.001 HIS A1059 PHE 0.024 0.002 PHE C 546 TYR 0.014 0.001 TYR B 523 ARG 0.004 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 395 time to evaluate : 4.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8664 (pt) cc_final: 0.8328 (pt) REVERT: A 113 MET cc_start: 0.8390 (mmm) cc_final: 0.7290 (mmm) REVERT: A 369 ARG cc_start: 0.7737 (ptm160) cc_final: 0.7499 (mtp85) REVERT: A 414 MET cc_start: 0.9131 (tpp) cc_final: 0.8823 (tpp) REVERT: A 450 TYR cc_start: 0.8627 (m-80) cc_final: 0.8291 (m-10) REVERT: A 527 MET cc_start: 0.8801 (ttt) cc_final: 0.8420 (mmp) REVERT: A 600 ILE cc_start: 0.9222 (tp) cc_final: 0.8787 (pt) REVERT: A 670 MET cc_start: 0.9161 (mtp) cc_final: 0.8796 (mtp) REVERT: A 1022 LEU cc_start: 0.7897 (tp) cc_final: 0.7661 (tp) REVERT: A 1082 PHE cc_start: 0.7950 (p90) cc_final: 0.6262 (t80) REVERT: B 126 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8905 (mp0) REVERT: B 361 MET cc_start: 0.7029 (mmp) cc_final: 0.6529 (mmm) REVERT: B 407 MET cc_start: 0.8965 (mtm) cc_final: 0.8617 (mtt) REVERT: B 414 MET cc_start: 0.8476 (mtm) cc_final: 0.8163 (ptp) REVERT: B 503 MET cc_start: 0.7178 (tmm) cc_final: 0.6760 (tmm) REVERT: B 519 ASP cc_start: 0.8340 (t0) cc_final: 0.8014 (t70) REVERT: B 670 MET cc_start: 0.8771 (mmm) cc_final: 0.8495 (tpp) REVERT: B 721 MET cc_start: 0.6740 (mmm) cc_final: 0.6482 (mmm) REVERT: B 729 SER cc_start: 0.8129 (m) cc_final: 0.7632 (t) REVERT: B 813 GLU cc_start: 0.8735 (tt0) cc_final: 0.8270 (tm-30) REVERT: B 816 TYR cc_start: 0.8346 (t80) cc_final: 0.7945 (t80) REVERT: B 1022 LEU cc_start: 0.8747 (tp) cc_final: 0.8385 (tp) REVERT: B 1027 VAL cc_start: 0.8481 (t) cc_final: 0.8218 (p) REVERT: B 1064 ARG cc_start: 0.6387 (mpt90) cc_final: 0.6088 (mmt180) REVERT: B 1191 MET cc_start: 0.8952 (tpp) cc_final: 0.8535 (tpp) REVERT: B 1195 LEU cc_start: 0.9571 (mm) cc_final: 0.9297 (mm) REVERT: B 1202 ASP cc_start: 0.8860 (m-30) cc_final: 0.8174 (t0) REVERT: C 113 MET cc_start: 0.8106 (mmm) cc_final: 0.7189 (mmm) REVERT: C 171 ASP cc_start: 0.9165 (m-30) cc_final: 0.8892 (t0) REVERT: C 431 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8920 (mp0) REVERT: C 600 ILE cc_start: 0.9152 (tp) cc_final: 0.8807 (pt) REVERT: C 670 MET cc_start: 0.9198 (mtp) cc_final: 0.8901 (mtp) REVERT: C 708 MET cc_start: 0.7966 (mmt) cc_final: 0.7426 (tpp) REVERT: C 1009 MET cc_start: 0.8541 (tpt) cc_final: 0.8322 (mtt) REVERT: C 1091 ASP cc_start: 0.7757 (m-30) cc_final: 0.7508 (m-30) REVERT: C 1191 MET cc_start: 0.8891 (mtt) cc_final: 0.8561 (mtp) REVERT: D 126 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8952 (mp0) REVERT: D 159 GLN cc_start: 0.7819 (mt0) cc_final: 0.7517 (mp10) REVERT: D 186 LEU cc_start: 0.9076 (mt) cc_final: 0.8774 (mt) REVERT: D 195 ASP cc_start: 0.7926 (t0) cc_final: 0.6043 (p0) REVERT: D 358 ILE cc_start: 0.8584 (mm) cc_final: 0.8143 (mm) REVERT: D 361 MET cc_start: 0.7339 (mmp) cc_final: 0.6940 (mmm) REVERT: D 503 MET cc_start: 0.7895 (tmm) cc_final: 0.7324 (tmm) REVERT: D 519 ASP cc_start: 0.8458 (t0) cc_final: 0.8131 (t70) REVERT: D 670 MET cc_start: 0.9075 (mtp) cc_final: 0.8737 (mmm) REVERT: D 713 GLU cc_start: 0.8688 (tt0) cc_final: 0.8487 (mt-10) REVERT: D 797 TYR cc_start: 0.8732 (m-10) cc_final: 0.8469 (m-10) REVERT: D 1022 LEU cc_start: 0.8589 (mt) cc_final: 0.8358 (tp) REVERT: D 1027 VAL cc_start: 0.7676 (t) cc_final: 0.7017 (p) REVERT: D 1202 ASP cc_start: 0.8907 (m-30) cc_final: 0.8421 (t0) outliers start: 1 outliers final: 0 residues processed: 396 average time/residue: 0.4137 time to fit residues: 269.2513 Evaluate side-chains 266 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 0.9990 chunk 268 optimal weight: 0.9990 chunk 185 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 239 optimal weight: 8.9990 chunk 357 optimal weight: 9.9990 chunk 378 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 339 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A1059 HIS B 46 HIS ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 642 GLN ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS D 46 HIS ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 642 GLN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 31840 Z= 0.333 Angle : 0.654 8.527 43034 Z= 0.347 Chirality : 0.044 0.230 4774 Planarity : 0.005 0.055 5408 Dihedral : 5.910 58.104 4388 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.93 % Favored : 93.04 % Rotamer: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.13), residues: 3910 helix: 0.76 (0.12), residues: 1754 sheet: -1.75 (0.24), residues: 426 loop : -1.72 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D1032 HIS 0.018 0.002 HIS A1059 PHE 0.030 0.002 PHE A 546 TYR 0.018 0.002 TYR A 797 ARG 0.007 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8597 (mmm) cc_final: 0.7267 (mmm) REVERT: A 450 TYR cc_start: 0.8753 (m-80) cc_final: 0.8340 (m-80) REVERT: A 527 MET cc_start: 0.8901 (ttt) cc_final: 0.8662 (mmt) REVERT: A 544 SER cc_start: 0.8343 (m) cc_final: 0.8025 (p) REVERT: A 600 ILE cc_start: 0.9330 (tp) cc_final: 0.8717 (pt) REVERT: A 670 MET cc_start: 0.9138 (mtp) cc_final: 0.8761 (mtp) REVERT: B 113 MET cc_start: 0.8323 (mmp) cc_final: 0.7372 (mpp) REVERT: B 126 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8827 (mp0) REVERT: B 151 ASP cc_start: 0.8586 (m-30) cc_final: 0.8380 (t0) REVERT: B 186 LEU cc_start: 0.9078 (mt) cc_final: 0.8863 (mt) REVERT: B 361 MET cc_start: 0.7236 (mmp) cc_final: 0.6733 (mmm) REVERT: B 407 MET cc_start: 0.8600 (mtt) cc_final: 0.8392 (mtt) REVERT: B 503 MET cc_start: 0.7191 (tmm) cc_final: 0.6643 (tmm) REVERT: B 519 ASP cc_start: 0.8455 (t0) cc_final: 0.8178 (t70) REVERT: B 729 SER cc_start: 0.7894 (m) cc_final: 0.7581 (t) REVERT: B 816 TYR cc_start: 0.8340 (t80) cc_final: 0.8075 (t80) REVERT: B 1116 MET cc_start: 0.8747 (ttm) cc_final: 0.8513 (ttm) REVERT: B 1191 MET cc_start: 0.9020 (tpp) cc_final: 0.8620 (tpp) REVERT: B 1195 LEU cc_start: 0.9541 (mm) cc_final: 0.9228 (mm) REVERT: B 1202 ASP cc_start: 0.8889 (m-30) cc_final: 0.8206 (t0) REVERT: C 113 MET cc_start: 0.8509 (mmm) cc_final: 0.7362 (mmm) REVERT: C 431 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8923 (mp0) REVERT: C 600 ILE cc_start: 0.9297 (tp) cc_final: 0.8796 (pt) REVERT: C 670 MET cc_start: 0.9233 (mtp) cc_final: 0.8849 (mtp) REVERT: C 1009 MET cc_start: 0.8869 (tpt) cc_final: 0.8455 (mtt) REVERT: C 1091 ASP cc_start: 0.7874 (m-30) cc_final: 0.7666 (m-30) REVERT: C 1190 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8567 (mt-10) REVERT: D 113 MET cc_start: 0.8571 (mmp) cc_final: 0.7585 (mpp) REVERT: D 126 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8859 (mp0) REVERT: D 186 LEU cc_start: 0.9135 (mt) cc_final: 0.8863 (mt) REVERT: D 299 LEU cc_start: 0.7980 (tp) cc_final: 0.7719 (mt) REVERT: D 361 MET cc_start: 0.7655 (mmp) cc_final: 0.7165 (mmm) REVERT: D 503 MET cc_start: 0.8054 (tmm) cc_final: 0.7349 (tmm) REVERT: D 519 ASP cc_start: 0.8663 (t0) cc_final: 0.8316 (t70) REVERT: D 1022 LEU cc_start: 0.8375 (mt) cc_final: 0.8164 (tp) REVERT: D 1191 MET cc_start: 0.9061 (tpp) cc_final: 0.8788 (tpp) REVERT: D 1202 ASP cc_start: 0.8888 (m-30) cc_final: 0.8384 (t0) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.4237 time to fit residues: 238.3643 Evaluate side-chains 224 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 323 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN C 355 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31840 Z= 0.272 Angle : 0.576 7.631 43034 Z= 0.307 Chirality : 0.041 0.176 4774 Planarity : 0.004 0.057 5408 Dihedral : 5.530 54.407 4388 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3910 helix: 1.03 (0.12), residues: 1754 sheet: -1.49 (0.26), residues: 384 loop : -1.68 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.013 0.001 HIS D1059 PHE 0.027 0.002 PHE C 546 TYR 0.023 0.001 TYR D 523 ARG 0.009 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8602 (mmm) cc_final: 0.7711 (mmm) REVERT: A 450 TYR cc_start: 0.8774 (m-80) cc_final: 0.8444 (m-80) REVERT: A 483 LEU cc_start: 0.8909 (tp) cc_final: 0.8695 (tt) REVERT: A 541 PHE cc_start: 0.9123 (t80) cc_final: 0.8920 (t80) REVERT: A 544 SER cc_start: 0.8290 (m) cc_final: 0.7957 (p) REVERT: A 600 ILE cc_start: 0.9340 (tp) cc_final: 0.8793 (pt) REVERT: A 670 MET cc_start: 0.9121 (mtp) cc_final: 0.8791 (mtp) REVERT: A 1091 ASP cc_start: 0.8090 (m-30) cc_final: 0.7890 (m-30) REVERT: B 113 MET cc_start: 0.8240 (mmp) cc_final: 0.7230 (mpp) REVERT: B 126 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8818 (mp0) REVERT: B 186 LEU cc_start: 0.9018 (mt) cc_final: 0.8756 (mt) REVERT: B 195 ASP cc_start: 0.7302 (t70) cc_final: 0.5861 (p0) REVERT: B 361 MET cc_start: 0.7319 (mmp) cc_final: 0.6794 (mmm) REVERT: B 407 MET cc_start: 0.8598 (mtt) cc_final: 0.8309 (mtt) REVERT: B 519 ASP cc_start: 0.8649 (t0) cc_final: 0.8323 (t70) REVERT: B 721 MET cc_start: 0.7135 (mtm) cc_final: 0.6794 (mtm) REVERT: B 729 SER cc_start: 0.7680 (m) cc_final: 0.7353 (t) REVERT: B 816 TYR cc_start: 0.8353 (t80) cc_final: 0.8090 (t80) REVERT: B 1116 MET cc_start: 0.8778 (ttm) cc_final: 0.8567 (ttm) REVERT: B 1191 MET cc_start: 0.8956 (tpp) cc_final: 0.8589 (tpp) REVERT: B 1195 LEU cc_start: 0.9574 (mm) cc_final: 0.9329 (mm) REVERT: B 1202 ASP cc_start: 0.8930 (m-30) cc_final: 0.8271 (t0) REVERT: C 113 MET cc_start: 0.8414 (mmm) cc_final: 0.7624 (mmm) REVERT: C 431 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8946 (mm-30) REVERT: C 544 SER cc_start: 0.7898 (m) cc_final: 0.7621 (p) REVERT: C 600 ILE cc_start: 0.9287 (tp) cc_final: 0.8761 (pt) REVERT: C 670 MET cc_start: 0.9253 (mtp) cc_final: 0.8914 (mtp) REVERT: C 708 MET cc_start: 0.7951 (mmt) cc_final: 0.7470 (mmm) REVERT: C 1009 MET cc_start: 0.9010 (tpt) cc_final: 0.8401 (mtt) REVERT: C 1091 ASP cc_start: 0.7759 (m-30) cc_final: 0.7523 (m-30) REVERT: C 1191 MET cc_start: 0.8892 (mtt) cc_final: 0.8513 (mtp) REVERT: D 113 MET cc_start: 0.8514 (mmp) cc_final: 0.7564 (mpp) REVERT: D 126 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8854 (mp0) REVERT: D 186 LEU cc_start: 0.9183 (mt) cc_final: 0.8924 (mt) REVERT: D 195 ASP cc_start: 0.7962 (t70) cc_final: 0.6540 (p0) REVERT: D 361 MET cc_start: 0.7635 (mmp) cc_final: 0.7264 (mmm) REVERT: D 463 MET cc_start: 0.7975 (ptp) cc_final: 0.7688 (mtt) REVERT: D 519 ASP cc_start: 0.8922 (t0) cc_final: 0.8601 (t70) REVERT: D 721 MET cc_start: 0.7488 (mmm) cc_final: 0.7154 (mmm) REVERT: D 1191 MET cc_start: 0.8998 (tpp) cc_final: 0.8762 (tpp) REVERT: D 1202 ASP cc_start: 0.8880 (m-30) cc_final: 0.8342 (t0) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.4001 time to fit residues: 201.8639 Evaluate side-chains 219 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 5.9990 chunk 341 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 222 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 379 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 642 GLN ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN D 764 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 31840 Z= 0.353 Angle : 0.658 8.755 43034 Z= 0.348 Chirality : 0.044 0.201 4774 Planarity : 0.005 0.052 5408 Dihedral : 5.687 50.364 4388 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.83 (0.13), residues: 3910 helix: 0.84 (0.12), residues: 1766 sheet: -1.64 (0.24), residues: 420 loop : -1.75 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1032 HIS 0.011 0.001 HIS A1059 PHE 0.031 0.002 PHE A 546 TYR 0.022 0.002 TYR C 523 ARG 0.004 0.001 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8644 (mmm) cc_final: 0.7692 (mmm) REVERT: A 450 TYR cc_start: 0.8919 (m-80) cc_final: 0.8445 (m-80) REVERT: A 600 ILE cc_start: 0.9355 (tp) cc_final: 0.8763 (pt) REVERT: A 670 MET cc_start: 0.9154 (mtp) cc_final: 0.8720 (mtp) REVERT: A 1010 LEU cc_start: 0.8669 (mp) cc_final: 0.8452 (mm) REVERT: A 1091 ASP cc_start: 0.8071 (m-30) cc_final: 0.7849 (m-30) REVERT: A 1191 MET cc_start: 0.8915 (mtt) cc_final: 0.8539 (mtt) REVERT: B 113 MET cc_start: 0.8358 (mmp) cc_final: 0.7163 (mpp) REVERT: B 126 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8717 (mp0) REVERT: B 195 ASP cc_start: 0.7613 (t70) cc_final: 0.5984 (p0) REVERT: B 361 MET cc_start: 0.7409 (mmp) cc_final: 0.6965 (mmm) REVERT: B 503 MET cc_start: 0.7090 (tmm) cc_final: 0.6783 (tmm) REVERT: B 729 SER cc_start: 0.7676 (m) cc_final: 0.7329 (t) REVERT: B 1116 MET cc_start: 0.8849 (ttm) cc_final: 0.8593 (ttm) REVERT: B 1191 MET cc_start: 0.8947 (tpp) cc_final: 0.8533 (tpp) REVERT: B 1195 LEU cc_start: 0.9565 (mm) cc_final: 0.9309 (mm) REVERT: B 1202 ASP cc_start: 0.8909 (m-30) cc_final: 0.8221 (t0) REVERT: C 113 MET cc_start: 0.8488 (mmm) cc_final: 0.7682 (mmm) REVERT: C 414 MET cc_start: 0.9233 (tpt) cc_final: 0.8909 (mpp) REVERT: C 544 SER cc_start: 0.8079 (m) cc_final: 0.7710 (p) REVERT: C 549 TYR cc_start: 0.7897 (t80) cc_final: 0.7664 (t80) REVERT: C 600 ILE cc_start: 0.9336 (tp) cc_final: 0.8782 (pt) REVERT: C 670 MET cc_start: 0.9158 (mtp) cc_final: 0.8923 (mtp) REVERT: C 1009 MET cc_start: 0.9122 (tpt) cc_final: 0.8421 (mtt) REVERT: C 1069 GLU cc_start: 0.7735 (tp30) cc_final: 0.7527 (tp30) REVERT: C 1091 ASP cc_start: 0.7841 (m-30) cc_final: 0.7632 (m-30) REVERT: D 113 MET cc_start: 0.8682 (mmp) cc_final: 0.7597 (mpp) REVERT: D 126 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8821 (mp0) REVERT: D 186 LEU cc_start: 0.9165 (mt) cc_final: 0.8909 (mt) REVERT: D 195 ASP cc_start: 0.8178 (t70) cc_final: 0.6629 (p0) REVERT: D 361 MET cc_start: 0.7913 (mmp) cc_final: 0.7434 (mmm) REVERT: D 503 MET cc_start: 0.7891 (tmm) cc_final: 0.7459 (tmm) REVERT: D 721 MET cc_start: 0.7671 (mmm) cc_final: 0.7342 (mmm) REVERT: D 1191 MET cc_start: 0.8943 (tpp) cc_final: 0.8604 (tpp) REVERT: D 1202 ASP cc_start: 0.8834 (m-30) cc_final: 0.8310 (t0) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.3728 time to fit residues: 174.4778 Evaluate side-chains 216 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.0060 chunk 42 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 377 optimal weight: 8.9990 chunk 236 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN B 764 ASN B1059 HIS C 24 GLN C 355 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31840 Z= 0.160 Angle : 0.513 8.572 43034 Z= 0.271 Chirality : 0.040 0.206 4774 Planarity : 0.004 0.052 5408 Dihedral : 5.069 46.990 4388 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.36 (0.14), residues: 3910 helix: 1.30 (0.13), residues: 1772 sheet: -1.20 (0.27), residues: 368 loop : -1.68 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C1032 HIS 0.011 0.001 HIS A1059 PHE 0.016 0.001 PHE C 541 TYR 0.018 0.001 TYR D 523 ARG 0.006 0.000 ARG B 684 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8481 (pt) cc_final: 0.8207 (pt) REVERT: A 51 GLU cc_start: 0.8033 (pm20) cc_final: 0.7656 (tt0) REVERT: A 113 MET cc_start: 0.8559 (mmm) cc_final: 0.7451 (mmm) REVERT: A 450 TYR cc_start: 0.8842 (m-80) cc_final: 0.8458 (m-80) REVERT: A 483 LEU cc_start: 0.9020 (tp) cc_final: 0.8766 (tt) REVERT: A 544 SER cc_start: 0.8407 (m) cc_final: 0.8018 (p) REVERT: A 600 ILE cc_start: 0.9341 (tp) cc_final: 0.8789 (pt) REVERT: A 670 MET cc_start: 0.9136 (mtp) cc_final: 0.8882 (mtp) REVERT: A 1010 LEU cc_start: 0.8604 (mp) cc_final: 0.8358 (mm) REVERT: A 1120 CYS cc_start: 0.6720 (t) cc_final: 0.6443 (m) REVERT: A 1191 MET cc_start: 0.8872 (mtt) cc_final: 0.8459 (mtt) REVERT: B 113 MET cc_start: 0.8208 (mmp) cc_final: 0.7010 (mpp) REVERT: B 126 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8879 (pt0) REVERT: B 186 LEU cc_start: 0.9061 (mt) cc_final: 0.8842 (mt) REVERT: B 361 MET cc_start: 0.7658 (mmp) cc_final: 0.7018 (mmm) REVERT: B 463 MET cc_start: 0.8010 (ptp) cc_final: 0.7791 (mtt) REVERT: B 503 MET cc_start: 0.7273 (tmm) cc_final: 0.6937 (tmm) REVERT: B 729 SER cc_start: 0.7673 (m) cc_final: 0.7349 (t) REVERT: B 1116 MET cc_start: 0.8893 (ttm) cc_final: 0.8682 (ttm) REVERT: B 1191 MET cc_start: 0.8945 (tpp) cc_final: 0.8532 (tpp) REVERT: B 1195 LEU cc_start: 0.9582 (mm) cc_final: 0.9323 (mm) REVERT: B 1202 ASP cc_start: 0.8850 (m-30) cc_final: 0.8167 (t0) REVERT: C 113 MET cc_start: 0.8405 (mmm) cc_final: 0.7389 (mmm) REVERT: C 414 MET cc_start: 0.9200 (tpt) cc_final: 0.8843 (mpp) REVERT: C 544 SER cc_start: 0.8043 (m) cc_final: 0.7662 (p) REVERT: C 549 TYR cc_start: 0.7918 (t80) cc_final: 0.7689 (t80) REVERT: C 600 ILE cc_start: 0.9249 (tp) cc_final: 0.8738 (pt) REVERT: C 670 MET cc_start: 0.9191 (mtp) cc_final: 0.8910 (mtp) REVERT: C 1009 MET cc_start: 0.9065 (tpt) cc_final: 0.8418 (mtt) REVERT: C 1191 MET cc_start: 0.8828 (mtt) cc_final: 0.8461 (mtp) REVERT: D 113 MET cc_start: 0.8495 (mmp) cc_final: 0.7304 (mpp) REVERT: D 186 LEU cc_start: 0.9140 (mt) cc_final: 0.8871 (mt) REVERT: D 361 MET cc_start: 0.7789 (mmp) cc_final: 0.7345 (mmm) REVERT: D 463 MET cc_start: 0.8208 (ptp) cc_final: 0.7234 (mtm) REVERT: D 503 MET cc_start: 0.7907 (tmm) cc_final: 0.7443 (tmm) REVERT: D 721 MET cc_start: 0.7361 (mmm) cc_final: 0.7049 (mmm) REVERT: D 1022 LEU cc_start: 0.8119 (tp) cc_final: 0.7891 (tp) REVERT: D 1191 MET cc_start: 0.8939 (tpp) cc_final: 0.8617 (tpp) REVERT: D 1202 ASP cc_start: 0.8869 (m-30) cc_final: 0.8327 (t0) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.3702 time to fit residues: 185.6184 Evaluate side-chains 224 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 225 optimal weight: 0.0020 chunk 113 optimal weight: 0.0670 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 overall best weight: 0.8928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN C 24 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31840 Z= 0.143 Angle : 0.495 9.712 43034 Z= 0.261 Chirality : 0.039 0.161 4774 Planarity : 0.004 0.051 5408 Dihedral : 4.805 45.627 4388 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.16 (0.14), residues: 3910 helix: 1.46 (0.13), residues: 1776 sheet: -1.04 (0.29), residues: 346 loop : -1.58 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C1032 HIS 0.014 0.001 HIS B1059 PHE 0.024 0.001 PHE C 546 TYR 0.016 0.001 TYR D 523 ARG 0.006 0.000 ARG B 684 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8523 (pt) cc_final: 0.8267 (pt) REVERT: A 51 GLU cc_start: 0.8086 (pm20) cc_final: 0.7730 (tt0) REVERT: A 113 MET cc_start: 0.8548 (mmm) cc_final: 0.7429 (mmm) REVERT: A 407 MET cc_start: 0.9078 (mmm) cc_final: 0.8864 (mmm) REVERT: A 450 TYR cc_start: 0.8775 (m-80) cc_final: 0.8467 (m-80) REVERT: A 541 PHE cc_start: 0.8920 (t80) cc_final: 0.8688 (t80) REVERT: A 544 SER cc_start: 0.8368 (m) cc_final: 0.7960 (p) REVERT: A 600 ILE cc_start: 0.9347 (tp) cc_final: 0.8809 (pt) REVERT: A 670 MET cc_start: 0.9206 (mtp) cc_final: 0.8828 (mtp) REVERT: A 1120 CYS cc_start: 0.6731 (t) cc_final: 0.6396 (m) REVERT: B 97 ILE cc_start: 0.8489 (mp) cc_final: 0.8160 (mp) REVERT: B 113 MET cc_start: 0.8202 (mmp) cc_final: 0.7160 (mpp) REVERT: B 126 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8835 (pt0) REVERT: B 186 LEU cc_start: 0.9049 (mt) cc_final: 0.8828 (mt) REVERT: B 195 ASP cc_start: 0.7457 (t0) cc_final: 0.5409 (p0) REVERT: B 361 MET cc_start: 0.7633 (mmp) cc_final: 0.6976 (mmm) REVERT: B 463 MET cc_start: 0.8027 (ptp) cc_final: 0.7774 (mtt) REVERT: B 503 MET cc_start: 0.7301 (tmm) cc_final: 0.6947 (tmm) REVERT: B 729 SER cc_start: 0.7675 (m) cc_final: 0.7338 (t) REVERT: B 1031 TYR cc_start: 0.6708 (p90) cc_final: 0.6323 (p90) REVERT: B 1116 MET cc_start: 0.8818 (ttm) cc_final: 0.8579 (ttm) REVERT: B 1191 MET cc_start: 0.8956 (tpp) cc_final: 0.8513 (tpp) REVERT: B 1195 LEU cc_start: 0.9574 (mm) cc_final: 0.9319 (mm) REVERT: B 1202 ASP cc_start: 0.8827 (m-30) cc_final: 0.8165 (t0) REVERT: C 50 LEU cc_start: 0.8579 (pt) cc_final: 0.8349 (pt) REVERT: C 113 MET cc_start: 0.8388 (mmm) cc_final: 0.7366 (mmm) REVERT: C 414 MET cc_start: 0.9204 (tpt) cc_final: 0.8816 (mpp) REVERT: C 544 SER cc_start: 0.8053 (m) cc_final: 0.7672 (p) REVERT: C 549 TYR cc_start: 0.7869 (t80) cc_final: 0.7661 (t80) REVERT: C 600 ILE cc_start: 0.9249 (tp) cc_final: 0.8752 (pt) REVERT: C 1009 MET cc_start: 0.9088 (tpt) cc_final: 0.8526 (mtt) REVERT: C 1191 MET cc_start: 0.8813 (mtt) cc_final: 0.8448 (mtp) REVERT: D 113 MET cc_start: 0.8493 (mmp) cc_final: 0.7245 (mpp) REVERT: D 126 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8831 (mp0) REVERT: D 186 LEU cc_start: 0.9135 (mt) cc_final: 0.8870 (mt) REVERT: D 195 ASP cc_start: 0.8160 (t0) cc_final: 0.6151 (p0) REVERT: D 361 MET cc_start: 0.7829 (mmp) cc_final: 0.7399 (mmm) REVERT: D 463 MET cc_start: 0.8201 (ptp) cc_final: 0.7171 (mtt) REVERT: D 503 MET cc_start: 0.7940 (tmm) cc_final: 0.7507 (tmm) REVERT: D 721 MET cc_start: 0.7272 (mmm) cc_final: 0.6988 (mmm) REVERT: D 1191 MET cc_start: 0.8938 (tpp) cc_final: 0.8632 (tpp) REVERT: D 1202 ASP cc_start: 0.8881 (m-30) cc_final: 0.8323 (t0) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.3716 time to fit residues: 185.1611 Evaluate side-chains 220 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.9980 chunk 361 optimal weight: 0.9990 chunk 330 optimal weight: 0.0970 chunk 352 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 318 optimal weight: 4.9990 chunk 332 optimal weight: 0.8980 chunk 350 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 642 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN D 642 GLN D 791 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.6966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31840 Z= 0.130 Angle : 0.480 8.902 43034 Z= 0.251 Chirality : 0.039 0.150 4774 Planarity : 0.003 0.050 5408 Dihedral : 4.533 40.913 4388 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3910 helix: 1.55 (0.13), residues: 1784 sheet: -0.86 (0.29), residues: 350 loop : -1.51 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1032 HIS 0.013 0.001 HIS B1059 PHE 0.023 0.001 PHE C 546 TYR 0.015 0.001 TYR D 523 ARG 0.006 0.000 ARG B 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8587 (pt) cc_final: 0.8377 (pt) REVERT: A 51 GLU cc_start: 0.8093 (pm20) cc_final: 0.7736 (tt0) REVERT: A 113 MET cc_start: 0.8481 (mmm) cc_final: 0.7361 (mmm) REVERT: A 407 MET cc_start: 0.8963 (mmm) cc_final: 0.8723 (mmm) REVERT: A 450 TYR cc_start: 0.8797 (m-80) cc_final: 0.8470 (m-80) REVERT: A 541 PHE cc_start: 0.8859 (t80) cc_final: 0.8632 (t80) REVERT: A 544 SER cc_start: 0.8500 (m) cc_final: 0.8104 (p) REVERT: A 600 ILE cc_start: 0.9327 (tp) cc_final: 0.8829 (pt) REVERT: A 670 MET cc_start: 0.9175 (mtp) cc_final: 0.8817 (mtp) REVERT: A 1120 CYS cc_start: 0.6875 (t) cc_final: 0.6649 (m) REVERT: A 1191 MET cc_start: 0.8738 (mtt) cc_final: 0.8398 (mpp) REVERT: A 1199 MET cc_start: 0.8880 (tpp) cc_final: 0.8605 (mtt) REVERT: B 113 MET cc_start: 0.8209 (mmp) cc_final: 0.7839 (mmm) REVERT: B 126 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8816 (pt0) REVERT: B 186 LEU cc_start: 0.9038 (mt) cc_final: 0.8819 (mt) REVERT: B 195 ASP cc_start: 0.7325 (t0) cc_final: 0.5372 (p0) REVERT: B 361 MET cc_start: 0.7673 (mmp) cc_final: 0.7059 (mmm) REVERT: B 407 MET cc_start: 0.8887 (mtt) cc_final: 0.8463 (mpp) REVERT: B 454 ASP cc_start: 0.7903 (t0) cc_final: 0.7626 (m-30) REVERT: B 463 MET cc_start: 0.8050 (ptp) cc_final: 0.7717 (mtt) REVERT: B 503 MET cc_start: 0.7128 (tmm) cc_final: 0.6790 (tmm) REVERT: B 729 SER cc_start: 0.7713 (m) cc_final: 0.7419 (t) REVERT: B 1031 TYR cc_start: 0.6547 (p90) cc_final: 0.6171 (p90) REVERT: B 1116 MET cc_start: 0.8817 (ttm) cc_final: 0.8591 (ttm) REVERT: B 1191 MET cc_start: 0.8918 (tpp) cc_final: 0.8483 (tpp) REVERT: B 1195 LEU cc_start: 0.9572 (mm) cc_final: 0.9311 (mm) REVERT: B 1202 ASP cc_start: 0.8799 (m-30) cc_final: 0.8121 (t0) REVERT: C 113 MET cc_start: 0.8443 (mmm) cc_final: 0.7457 (mmm) REVERT: C 414 MET cc_start: 0.9219 (tpt) cc_final: 0.8825 (mpp) REVERT: C 544 SER cc_start: 0.8105 (m) cc_final: 0.7721 (p) REVERT: C 600 ILE cc_start: 0.9209 (tp) cc_final: 0.8774 (pt) REVERT: C 629 MET cc_start: 0.4632 (ppp) cc_final: 0.4374 (ppp) REVERT: C 1009 MET cc_start: 0.9164 (tpt) cc_final: 0.8476 (mtt) REVERT: C 1191 MET cc_start: 0.8869 (mtt) cc_final: 0.8481 (mtp) REVERT: C 1199 MET cc_start: 0.9088 (tpp) cc_final: 0.8620 (mtt) REVERT: D 186 LEU cc_start: 0.9145 (mt) cc_final: 0.8883 (mt) REVERT: D 195 ASP cc_start: 0.8099 (t0) cc_final: 0.6114 (p0) REVERT: D 245 PHE cc_start: 0.8425 (m-80) cc_final: 0.8218 (m-10) REVERT: D 361 MET cc_start: 0.7860 (mmp) cc_final: 0.7438 (mmm) REVERT: D 463 MET cc_start: 0.8179 (ptp) cc_final: 0.7144 (mtt) REVERT: D 503 MET cc_start: 0.7953 (tmm) cc_final: 0.7513 (tmm) REVERT: D 508 GLN cc_start: 0.7185 (pm20) cc_final: 0.6937 (tp-100) REVERT: D 721 MET cc_start: 0.7221 (mmm) cc_final: 0.6917 (mmm) REVERT: D 1191 MET cc_start: 0.8891 (tpp) cc_final: 0.8647 (tpp) REVERT: D 1202 ASP cc_start: 0.8918 (m-30) cc_final: 0.8390 (t0) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.3824 time to fit residues: 199.3113 Evaluate side-chains 226 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.9990 chunk 372 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 390 optimal weight: 4.9990 chunk 359 optimal weight: 0.0970 chunk 310 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.7046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31840 Z= 0.145 Angle : 0.490 7.525 43034 Z= 0.256 Chirality : 0.039 0.156 4774 Planarity : 0.003 0.051 5408 Dihedral : 4.483 38.845 4388 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3910 helix: 1.61 (0.13), residues: 1784 sheet: -0.76 (0.28), residues: 360 loop : -1.45 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1032 HIS 0.011 0.001 HIS B1059 PHE 0.026 0.001 PHE A 546 TYR 0.015 0.001 TYR D 523 ARG 0.005 0.000 ARG B 684 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8575 (pt) cc_final: 0.8359 (pt) REVERT: A 51 GLU cc_start: 0.8103 (pm20) cc_final: 0.7734 (tt0) REVERT: A 113 MET cc_start: 0.8566 (mmm) cc_final: 0.7462 (mmm) REVERT: A 407 MET cc_start: 0.8934 (mmm) cc_final: 0.8698 (mmm) REVERT: A 450 TYR cc_start: 0.8809 (m-80) cc_final: 0.8473 (m-80) REVERT: A 541 PHE cc_start: 0.8876 (t80) cc_final: 0.8631 (t80) REVERT: A 544 SER cc_start: 0.8494 (m) cc_final: 0.8059 (p) REVERT: A 600 ILE cc_start: 0.9329 (tp) cc_final: 0.8834 (pt) REVERT: A 670 MET cc_start: 0.9181 (mtp) cc_final: 0.8827 (mtp) REVERT: A 1120 CYS cc_start: 0.6908 (t) cc_final: 0.6664 (m) REVERT: A 1191 MET cc_start: 0.8761 (mtt) cc_final: 0.8402 (mpp) REVERT: A 1199 MET cc_start: 0.8875 (tpp) cc_final: 0.8545 (mtt) REVERT: B 113 MET cc_start: 0.8239 (mmp) cc_final: 0.7011 (mpp) REVERT: B 126 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8851 (pt0) REVERT: B 186 LEU cc_start: 0.9038 (mt) cc_final: 0.8821 (mt) REVERT: B 195 ASP cc_start: 0.7403 (t0) cc_final: 0.5410 (p0) REVERT: B 361 MET cc_start: 0.7637 (mmp) cc_final: 0.6986 (mmm) REVERT: B 407 MET cc_start: 0.8882 (mtt) cc_final: 0.8637 (mtt) REVERT: B 463 MET cc_start: 0.8048 (ptp) cc_final: 0.7729 (mtt) REVERT: B 503 MET cc_start: 0.7178 (tmm) cc_final: 0.6831 (tmm) REVERT: B 729 SER cc_start: 0.7724 (m) cc_final: 0.7422 (t) REVERT: B 1116 MET cc_start: 0.8797 (ttm) cc_final: 0.8565 (ttm) REVERT: B 1191 MET cc_start: 0.8907 (tpp) cc_final: 0.8443 (tpp) REVERT: B 1195 LEU cc_start: 0.9576 (mm) cc_final: 0.9302 (mm) REVERT: B 1202 ASP cc_start: 0.8818 (m-30) cc_final: 0.8158 (t0) REVERT: C 113 MET cc_start: 0.8485 (mmm) cc_final: 0.7540 (mmm) REVERT: C 414 MET cc_start: 0.9222 (tpt) cc_final: 0.8827 (mpp) REVERT: C 544 SER cc_start: 0.8094 (m) cc_final: 0.7683 (p) REVERT: C 600 ILE cc_start: 0.9220 (tp) cc_final: 0.8768 (pt) REVERT: C 629 MET cc_start: 0.4434 (ppp) cc_final: 0.4183 (ppp) REVERT: C 670 MET cc_start: 0.9171 (mtp) cc_final: 0.8936 (mtp) REVERT: C 1009 MET cc_start: 0.9139 (tpt) cc_final: 0.8374 (mtt) REVERT: C 1199 MET cc_start: 0.9050 (tpp) cc_final: 0.8628 (mtt) REVERT: D 186 LEU cc_start: 0.9151 (mt) cc_final: 0.8889 (mt) REVERT: D 195 ASP cc_start: 0.8124 (t0) cc_final: 0.6166 (p0) REVERT: D 361 MET cc_start: 0.7870 (mmp) cc_final: 0.7445 (mmm) REVERT: D 463 MET cc_start: 0.8204 (ptp) cc_final: 0.7178 (mtt) REVERT: D 503 MET cc_start: 0.8027 (tmm) cc_final: 0.7577 (tmm) REVERT: D 721 MET cc_start: 0.7257 (mmm) cc_final: 0.6939 (mmm) REVERT: D 1191 MET cc_start: 0.8849 (tpp) cc_final: 0.8617 (tpp) REVERT: D 1202 ASP cc_start: 0.8857 (m-30) cc_final: 0.8339 (t0) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.3661 time to fit residues: 182.2275 Evaluate side-chains 223 residues out of total 3348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.8980 chunk 331 optimal weight: 0.1980 chunk 95 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 311 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN D1078 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.087375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.066137 restraints weight = 112771.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.067048 restraints weight = 68433.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.067006 restraints weight = 55136.097| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31840 Z= 0.222 Angle : 0.538 7.728 43034 Z= 0.282 Chirality : 0.040 0.184 4774 Planarity : 0.004 0.063 5408 Dihedral : 4.648 38.391 4388 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3910 helix: 1.59 (0.13), residues: 1784 sheet: -0.85 (0.27), residues: 380 loop : -1.49 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1032 HIS 0.010 0.001 HIS C1059 PHE 0.027 0.001 PHE C 546 TYR 0.016 0.001 TYR D 523 ARG 0.005 0.000 ARG B 684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5831.85 seconds wall clock time: 106 minutes 39.80 seconds (6399.80 seconds total)