Starting phenix.real_space_refine on Wed Feb 21 19:39:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uia_20784/02_2024/6uia_20784_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uia_20784/02_2024/6uia_20784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uia_20784/02_2024/6uia_20784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uia_20784/02_2024/6uia_20784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uia_20784/02_2024/6uia_20784_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uia_20784/02_2024/6uia_20784_updated.pdb" } resolution = 4.3 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 ------------------------------------------------------------------------------- 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= 0.003 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 P 6 5.49 5 S 178 5.16 5 C 20298 2.51 5 N 5374 2.21 5 O 5864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C GLU 584": "OE1" <-> "OE2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C GLU 683": "OE1" <-> "OE2" Residue "C GLU 724": "OE1" <-> "OE2" Residue "C GLU 781": "OE1" <-> "OE2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 891": "OE1" <-> "OE2" Residue "C ARG 986": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1045": "NH1" <-> "NH2" Residue "C ARG 1085": "NH1" <-> "NH2" Residue "C GLU 1097": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D GLU 683": "OE1" <-> "OE2" Residue "D GLU 724": "OE1" <-> "OE2" Residue "D GLU 865": "OE1" <-> "OE2" Residue "D ARG 986": "NH1" <-> "NH2" Residue "D ARG 995": "NH1" <-> "NH2" Residue "D ARG 1045": "NH1" <-> "NH2" Residue "D ARG 1085": "NH1" <-> "NH2" Residue "D GLU 1097": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A GLU 866": "OE1" <-> "OE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A ARG 1045": "NH1" <-> "NH2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B GLU 683": "OE1" <-> "OE2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B GLU 792": "OE1" <-> "OE2" Residue "B ARG 986": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B GLU 1011": "OE1" <-> "OE2" Residue "B ARG 1045": "NH1" <-> "NH2" Residue "B GLU 1046": "OE1" <-> "OE2" Residue "B GLU 1050": "OE1" <-> "OE2" Residue "B ARG 1085": "NH1" <-> "NH2" Residue "B GLU 1097": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31720 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8058 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 30.01, per 1000 atoms: 0.95 Number of scatterers: 31720 At special positions: 0 Unit cell: (187.05, 171.39, 140.07, 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) S 178 16.00 P 6 15.00 O 5864 8.00 N 5374 7.00 C 20298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.43 Conformation dependent library (CDL) restraints added in 10.9 seconds 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 151 helices and 33 sheets defined 37.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.52 Creating SS restraints... Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 78 through 86 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 175 through 193 removed outlier: 5.123A pdb=" N GLU C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 181 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA C 182 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU C 193 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 removed outlier: 4.769A pdb=" N TYR C 227 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS C 230 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL C 231 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TRP C 233 " --> pdb=" O LYS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 259 Processing helix chain 'C' and resid 282 through 294 Processing helix chain 'C' and resid 313 through 326 Processing helix chain 'C' and resid 350 through 370 removed outlier: 3.621A pdb=" N ARG C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN C 365 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C 366 " --> pdb=" O ARG C 362 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'C' and resid 384 through 398 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 506 through 518 Processing helix chain 'C' and resid 556 through 562 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 643 through 648 Processing helix chain 'C' and resid 664 through 677 removed outlier: 3.608A pdb=" N ASN C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 706 Processing helix chain 'C' and resid 724 through 733 Processing helix chain 'C' and resid 772 through 780 Processing helix chain 'C' and resid 791 through 804 Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 869 through 876 Processing helix chain 'C' and resid 884 through 896 Processing helix chain 'C' and resid 905 through 915 Processing helix chain 'C' and resid 920 through 928 Processing helix chain 'C' and resid 938 through 950 removed outlier: 3.985A pdb=" N PHE C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 966 removed outlier: 4.814A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 966 " --> pdb=" O LYS C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 996 removed outlier: 3.804A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1016 removed outlier: 4.382A pdb=" N SER C1016 " --> pdb=" O LYS C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1039 removed outlier: 4.091A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1054 removed outlier: 3.566A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1078 removed outlier: 3.821A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1090 No H-bonds generated for 'chain 'C' and resid 1088 through 1090' Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 42 through 45 No H-bonds generated for 'chain 'D' and resid 42 through 45' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 79 through 86 Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 175 through 193 removed outlier: 4.992A pdb=" N GLU D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE D 180 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 181 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA D 182 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 6.271A pdb=" N VAL D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 259 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 313 through 326 Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 384 through 398 Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 506 through 518 Processing helix chain 'D' and resid 556 through 562 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 603 through 616 Processing helix chain 'D' and resid 643 through 648 Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 698 through 706 removed outlier: 3.989A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 772 through 780 Processing helix chain 'D' and resid 791 through 806 removed outlier: 3.676A pdb=" N GLY D 794 " --> pdb=" O ASP D 791 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 796 " --> pdb=" O LEU D 793 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 800 " --> pdb=" O ILE D 797 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 805 " --> pdb=" O GLU D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 830 Processing helix chain 'D' and resid 859 through 865 Processing helix chain 'D' and resid 869 through 876 Processing helix chain 'D' and resid 884 through 896 removed outlier: 3.563A pdb=" N GLN D 888 " --> pdb=" O LYS D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 915 Processing helix chain 'D' and resid 920 through 928 Processing helix chain 'D' and resid 938 through 951 removed outlier: 4.177A pdb=" N PHE D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 962 removed outlier: 4.690A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 994 Processing helix chain 'D' and resid 1002 through 1017 removed outlier: 3.679A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1039 removed outlier: 4.200A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1054 removed outlier: 3.544A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1078 removed outlier: 3.875A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 78 through 88 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 178 through 191 removed outlier: 5.461A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 249 through 259 Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.508A pdb=" N VAL A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 605 through 615 Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 665 through 676 removed outlier: 4.069A pdb=" N GLU A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 705 removed outlier: 3.761A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 791 through 806 removed outlier: 4.387A pdb=" N GLU A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 869 through 877 Processing helix chain 'A' and resid 884 through 896 removed outlier: 3.791A pdb=" N GLN A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 920 through 928 Processing helix chain 'A' and resid 938 through 950 removed outlier: 3.601A pdb=" N ALA A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 964 removed outlier: 4.532A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 994 Processing helix chain 'A' and resid 1002 through 1016 removed outlier: 4.082A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 4.218A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1054 Processing helix chain 'A' and resid 1058 through 1078 removed outlier: 4.286A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 42 through 45 No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 223 through 233 removed outlier: 4.578A pdb=" N TYR B 227 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS B 230 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL B 231 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TRP B 233 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 259 Processing helix chain 'B' and resid 282 through 294 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 350 through 361 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 384 through 398 Processing helix chain 'B' and resid 411 through 418 removed outlier: 4.119A pdb=" N ILE B 414 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 415 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 417 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 418 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 518 Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 575 through 586 removed outlier: 4.706A pdb=" N TYR B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP B 580 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 616 Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 697 through 704 Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 772 through 780 Processing helix chain 'B' and resid 790 through 806 removed outlier: 3.923A pdb=" N GLY B 794 " --> pdb=" O ASP B 791 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 796 " --> pdb=" O LEU B 793 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 797 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 800 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 805 " --> pdb=" O GLU B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 859 through 865 Processing helix chain 'B' and resid 869 through 877 Processing helix chain 'B' and resid 886 through 896 Processing helix chain 'B' and resid 905 through 915 Processing helix chain 'B' and resid 920 through 928 Processing helix chain 'B' and resid 938 through 950 removed outlier: 3.967A pdb=" N PHE B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 966 removed outlier: 4.623A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 Processing helix chain 'B' and resid 1002 through 1014 Processing helix chain 'B' and resid 1025 through 1039 removed outlier: 4.368A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1054 removed outlier: 3.517A pdb=" N GLU B1050 " --> pdb=" O GLU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1078 removed outlier: 3.960A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.400A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 32 through 35 Processing sheet with id= C, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= D, first strand: chain 'C' and resid 205 through 207 Processing sheet with id= E, first strand: chain 'C' and resid 263 through 268 Processing sheet with id= F, first strand: chain 'C' and resid 275 through 277 removed outlier: 5.834A pdb=" N ILE C 337 " --> pdb=" O TRP C 276 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 537 through 543 removed outlier: 8.390A pdb=" N ALA C 527 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 567 " --> pdb=" O LYS C 498 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE C 500 " --> pdb=" O ASP C 567 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU C 569 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TRP C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN C 571 " --> pdb=" O TRP C 502 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR C 593 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ASN C 571 " --> pdb=" O THR C 593 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA C 595 " --> pdb=" O ASN C 571 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 739 through 745 removed outlier: 7.645A pdb=" N TYR C 659 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY C 684 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N SER C 661 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA C 686 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 32 through 34 removed outlier: 3.805A pdb=" N GLU D 108 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 92 through 95 Processing sheet with id= K, first strand: chain 'D' and resid 218 through 221 removed outlier: 7.850A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 263 through 268 Processing sheet with id= M, first strand: chain 'D' and resid 275 through 278 removed outlier: 6.803A pdb=" N ILE D 337 " --> pdb=" O TRP D 276 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N MET D 278 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE D 339 " --> pdb=" O MET D 278 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 537 through 543 removed outlier: 8.443A pdb=" N ALA D 527 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE D 500 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU D 569 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP D 502 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN D 571 " --> pdb=" O TRP D 502 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR D 593 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN D 571 " --> pdb=" O THR D 593 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA D 595 " --> pdb=" O ASN D 571 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 627 through 629 removed outlier: 4.644A pdb=" N GLY D 627 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 686 " --> pdb=" O GLY D 627 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET D 712 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL D 660 " --> pdb=" O MET D 712 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 714 " --> pdb=" O VAL D 660 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL D 715 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL D 741 " --> pdb=" O VAL D 715 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N GLY D 717 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP D 743 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 32 through 34 Processing sheet with id= Q, first strand: chain 'A' and resid 93 through 95 Processing sheet with id= R, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.567A pdb=" N TYR A 120 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 199 through 202 Processing sheet with id= T, first strand: chain 'A' and resid 263 through 268 Processing sheet with id= U, first strand: chain 'A' and resid 275 through 277 removed outlier: 5.492A pdb=" N ILE A 337 " --> pdb=" O TRP A 276 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'A' and resid 499 through 502 removed outlier: 5.888A pdb=" N VAL A 568 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP A 502 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE A 570 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR A 593 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASN A 571 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA A 595 " --> pdb=" O ASN A 571 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'A' and resid 537 through 543 Processing sheet with id= X, first strand: chain 'A' and resid 739 through 744 removed outlier: 6.580A pdb=" N TYR A 659 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 684 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER A 661 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA A 686 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 32 through 34 Processing sheet with id= Z, first strand: chain 'B' and resid 93 through 95 Processing sheet with id= AA, first strand: chain 'B' and resid 218 through 221 removed outlier: 8.497A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 205 through 207 Processing sheet with id= AC, first strand: chain 'B' and resid 263 through 268 Processing sheet with id= AD, first strand: chain 'B' and resid 275 through 280 removed outlier: 6.422A pdb=" N ILE B 337 " --> pdb=" O TRP B 276 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N MET B 278 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE B 339 " --> pdb=" O MET B 278 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 280 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY B 341 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 342 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B 377 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N HIS B 403 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 499 through 502 removed outlier: 7.472A pdb=" N VAL B 568 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N TRP B 502 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE B 570 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR B 593 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASN B 571 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA B 595 " --> pdb=" O ASN B 571 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'B' and resid 528 through 530 removed outlier: 9.215A pdb=" N MET B 529 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 627 through 629 removed outlier: 4.445A pdb=" N GLY B 627 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 657 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY B 684 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR B 659 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA B 686 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER B 661 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N MET B 712 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL B 660 " --> pdb=" O MET B 712 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 714 " --> pdb=" O VAL B 660 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 715 " --> pdb=" O PRO B 739 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL B 741 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY B 717 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TRP B 743 " --> pdb=" O GLY B 717 " (cutoff:3.500A) 1112 hydrogen bonds defined for protein. 3057 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: 13.41 Time building geometry restraints manager: 13.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.79: 32234 1.79 - 2.41: 175 2.41 - 3.02: 1 3.02 - 3.64: 3 3.64 - 4.26: 2 Bond restraints: 32415 Sorted by residual: bond pdb=" AO6 COA A1201 " pdb=" AP2 COA A1201 " ideal model delta sigma weight residual 1.610 4.256 -2.646 2.00e-02 2.50e+03 1.75e+04 bond pdb=" AO6 COA B1201 " pdb=" AP2 COA B1201 " ideal model delta sigma weight residual 1.610 4.248 -2.638 2.00e-02 2.50e+03 1.74e+04 bond pdb=" AP1 COA A1201 " pdb="AO5* COA A1201 " ideal model delta sigma weight residual 1.610 3.158 -1.548 2.00e-02 2.50e+03 5.99e+03 bond pdb=" AP1 COA B1201 " pdb="AO5* COA B1201 " ideal model delta sigma weight residual 1.610 3.064 -1.454 2.00e-02 2.50e+03 5.29e+03 bond pdb=" CD1 TYR A 692 " pdb=" CE1 TYR A 692 " ideal model delta sigma weight residual 1.382 3.387 -2.005 3.00e-02 1.11e+03 4.47e+03 ... (remaining 32410 not shown) Histogram of bond angle deviations from ideal: 15.96 - 48.75: 2 48.75 - 81.54: 6 81.54 - 114.33: 19391 114.33 - 147.12: 24502 147.12 - 179.92: 6 Bond angle restraints: 43907 Sorted by residual: angle pdb=" C ARG A 127 " pdb=" N GLU A 128 " pdb=" CA GLU A 128 " ideal model delta sigma weight residual 120.89 165.48 -44.59 1.50e+00 4.44e-01 8.84e+02 angle pdb=" AO3 COA B1201 " pdb=" AP2 COA B1201 " pdb=" AO6 COA B1201 " ideal model delta sigma weight residual 102.60 15.96 86.64 3.00e+00 1.11e-01 8.34e+02 angle pdb=" AO3 COA A1201 " pdb=" AP2 COA A1201 " pdb=" AO6 COA A1201 " ideal model delta sigma weight residual 102.60 19.09 83.51 3.00e+00 1.11e-01 7.75e+02 angle pdb=" O PRO C 817 " pdb=" C PRO C 817 " pdb=" N PRO C 818 " ideal model delta sigma weight residual 121.15 130.82 -9.67 4.70e-01 4.53e+00 4.23e+02 angle pdb=" CA LEU A 368 " pdb=" CB LEU A 368 " pdb=" CG LEU A 368 " ideal model delta sigma weight residual 116.30 179.92 -63.62 3.50e+00 8.16e-02 3.30e+02 ... (remaining 43902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.07: 18276 27.07 - 54.13: 975 54.13 - 81.20: 101 81.20 - 108.26: 9 108.26 - 135.33: 4 Dihedral angle restraints: 19365 sinusoidal: 7726 harmonic: 11639 Sorted by residual: dihedral pdb=" CA VAL D 74 " pdb=" C VAL D 74 " pdb=" N ASN D 75 " pdb=" CA ASN D 75 " ideal model delta harmonic sigma weight residual 180.00 97.19 82.81 0 5.00e+00 4.00e-02 2.74e+02 dihedral pdb=" CA VAL D 72 " pdb=" C VAL D 72 " pdb=" N GLY D 73 " pdb=" CA GLY D 73 " ideal model delta harmonic sigma weight residual -180.00 -105.49 -74.51 0 5.00e+00 4.00e-02 2.22e+02 dihedral pdb=" CA VAL A 121 " pdb=" C VAL A 121 " pdb=" N CYS A 122 " pdb=" CA CYS A 122 " ideal model delta harmonic sigma weight residual 180.00 119.42 60.58 0 5.00e+00 4.00e-02 1.47e+02 ... (remaining 19362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 4852 0.302 - 0.603: 42 0.603 - 0.904: 1 0.904 - 1.206: 2 1.206 - 1.507: 3 Chirality restraints: 4900 Sorted by residual: chirality pdb=" CB THR A 328 " pdb=" CA THR A 328 " pdb=" OG1 THR A 328 " pdb=" CG2 THR A 328 " both_signs ideal model delta sigma weight residual False 2.55 1.04 1.51 2.00e-01 2.50e+01 5.68e+01 chirality pdb=" CB VAL D 74 " pdb=" CA VAL D 74 " pdb=" CG1 VAL D 74 " pdb=" CG2 VAL D 74 " both_signs ideal model delta sigma weight residual False -2.63 -1.18 -1.44 2.00e-01 2.50e+01 5.22e+01 chirality pdb=" CG LEU A 324 " pdb=" CB LEU A 324 " pdb=" CD1 LEU A 324 " pdb=" CD2 LEU A 324 " both_signs ideal model delta sigma weight residual False -2.59 -1.31 -1.28 2.00e-01 2.50e+01 4.10e+01 ... (remaining 4897 not shown) Planarity restraints: 5617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 366 " -0.106 5.00e-02 4.00e+02 1.62e-01 4.19e+01 pdb=" N PRO A 367 " 0.280 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " -0.095 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 120 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C TYR A 120 " -0.104 2.00e-02 2.50e+03 pdb=" O TYR A 120 " 0.039 2.00e-02 2.50e+03 pdb=" N VAL A 121 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 118 " -0.027 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" C GLU A 118 " 0.094 2.00e-02 2.50e+03 pdb=" O GLU A 118 " -0.034 2.00e-02 2.50e+03 pdb=" N PHE A 119 " -0.032 2.00e-02 2.50e+03 ... (remaining 5614 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 41 2.30 - 2.95: 13834 2.95 - 3.60: 47565 3.60 - 4.25: 76228 4.25 - 4.90: 121470 Nonbonded interactions: 259138 Sorted by model distance: nonbonded pdb=" AO6 COA A1201 " pdb=" AP1 COA A1201 " model vdw 1.651 2.720 nonbonded pdb=" AP2 COA B1201 " pdb="AO5* COA B1201 " model vdw 1.663 2.720 nonbonded pdb=" AO6 COA B1201 " pdb=" AP1 COA B1201 " model vdw 1.665 2.720 nonbonded pdb=" AP2 COA A1201 " pdb="AO5* COA A1201 " model vdw 1.677 2.720 nonbonded pdb=" OE2 GLU B 92 " pdb=" OG1 THR B 99 " model vdw 2.172 2.440 ... (remaining 259133 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 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 0.840 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: 4.290 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 104.150 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5066 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 : 0.032 2.646 32415 Z= 2.077 Angle : 1.885 86.643 43907 Z= 0.975 Chirality : 0.092 1.507 4900 Planarity : 0.010 0.162 5617 Dihedral : 16.034 135.329 11973 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.40 % Favored : 90.86 % Rotamer: Outliers : 1.60 % Allowed : 8.82 % Favored : 89.58 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 3.06 % Twisted General : 1.36 % 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: -4.29 (0.10), residues: 4066 helix: -2.97 (0.09), residues: 1598 sheet: -1.81 (0.22), residues: 436 loop : -2.98 (0.11), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.005 TRP D 84 HIS 0.029 0.004 HIS A 135 PHE 0.079 0.004 PHE D 110 TYR 0.057 0.004 TYR A 692 ARG 0.026 0.002 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 881 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 831 time to evaluate : 3.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 THR cc_start: 0.7420 (m) cc_final: 0.7189 (m) REVERT: C 194 ASP cc_start: 0.6850 (m-30) cc_final: 0.6563 (t0) REVERT: C 235 ASP cc_start: 0.7260 (p0) cc_final: 0.6810 (p0) REVERT: C 278 MET cc_start: 0.7356 (ttt) cc_final: 0.7052 (ttp) REVERT: C 391 MET cc_start: 0.6707 (ttp) cc_final: 0.6256 (ttp) REVERT: C 519 CYS cc_start: 0.7727 (m) cc_final: 0.7492 (p) REVERT: C 584 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7631 (tm-30) REVERT: C 687 ILE cc_start: 0.8541 (pt) cc_final: 0.8056 (mt) REVERT: C 704 TYR cc_start: 0.7438 (m-10) cc_final: 0.7126 (m-10) REVERT: D 404 VAL cc_start: 0.7609 (m) cc_final: 0.7217 (m) REVERT: D 618 VAL cc_start: 0.7322 (t) cc_final: 0.6950 (t) REVERT: D 869 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (pt) REVERT: D 1079 LEU cc_start: 0.8460 (mp) cc_final: 0.7792 (tp) REVERT: A 208 THR cc_start: 0.3105 (OUTLIER) cc_final: 0.2306 (m) REVERT: A 566 VAL cc_start: -0.2066 (OUTLIER) cc_final: -0.2270 (m) REVERT: A 625 THR cc_start: 0.4957 (t) cc_final: 0.4648 (t) REVERT: A 715 VAL cc_start: 0.3744 (OUTLIER) cc_final: 0.3152 (t) REVERT: A 867 MET cc_start: 0.6562 (ptp) cc_final: 0.6281 (mtm) REVERT: A 873 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.6514 (mt) REVERT: A 915 ARG cc_start: 0.7026 (ttt180) cc_final: 0.6647 (mtp85) REVERT: A 990 LEU cc_start: 0.9312 (tp) cc_final: 0.9099 (tp) REVERT: B 353 THR cc_start: 0.7808 (p) cc_final: 0.7511 (m) REVERT: B 497 THR cc_start: 0.6399 (m) cc_final: 0.4993 (p) REVERT: B 580 ASP cc_start: 0.7478 (m-30) cc_final: 0.6811 (m-30) REVERT: B 651 LEU cc_start: 0.8371 (mt) cc_final: 0.8113 (mt) REVERT: B 843 SER cc_start: 0.8708 (m) cc_final: 0.8427 (p) REVERT: B 869 ILE cc_start: 0.8351 (pt) cc_final: 0.7918 (pt) REVERT: B 873 LEU cc_start: 0.8706 (mp) cc_final: 0.7707 (tp) REVERT: B 959 PHE cc_start: 0.7764 (t80) cc_final: 0.7301 (t80) REVERT: B 1052 ILE cc_start: 0.8507 (mm) cc_final: 0.8178 (mm) outliers start: 50 outliers final: 12 residues processed: 871 average time/residue: 0.4735 time to fit residues: 635.0887 Evaluate side-chains 455 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 438 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 2.9990 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 30.0000 chunk 370 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 GLN C 61 GLN C 104 ASN C 314 GLN C 555 ASN C 563 HIS C 638 ASN C 705 GLN C 850 GLN C 908 HIS C 961 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 332 HIS D 421 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 HIS D 961 ASN D 982 ASN D 996 GLN D 997 HIS A 135 HIS A 150 GLN A 299 ASN A 314 GLN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS A 900 HIS A 908 HIS A 961 ASN A1076 GLN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN B 900 HIS B 908 HIS B 988 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5243 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.774 32415 Z= 0.914 Angle : 1.045 37.841 43907 Z= 0.539 Chirality : 0.057 0.686 4900 Planarity : 0.007 0.180 5617 Dihedral : 9.293 127.739 4473 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.45 % Favored : 91.23 % Rotamer: Outliers : 0.36 % Allowed : 4.42 % Favored : 95.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.46 % 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: -3.39 (0.11), residues: 4066 helix: -1.84 (0.11), residues: 1627 sheet: -1.63 (0.23), residues: 459 loop : -2.76 (0.12), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 84 HIS 0.014 0.002 HIS D 421 PHE 0.049 0.002 PHE C 189 TYR 0.061 0.002 TYR A 692 ARG 0.016 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 548 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 540 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: C 10 THR cc_start: 0.7217 (m) cc_final: 0.6893 (m) REVERT: C 194 ASP cc_start: 0.7251 (m-30) cc_final: 0.6737 (t0) REVERT: C 412 THR cc_start: 0.6297 (p) cc_final: 0.6060 (t) REVERT: C 582 THR cc_start: 0.9001 (p) cc_final: 0.8764 (t) REVERT: C 704 TYR cc_start: 0.7234 (m-10) cc_final: 0.6973 (m-10) REVERT: C 705 GLN cc_start: 0.5212 (OUTLIER) cc_final: 0.4696 (tm-30) REVERT: C 877 TRP cc_start: 0.7499 (m-10) cc_final: 0.7252 (m-10) REVERT: C 895 MET cc_start: 0.8125 (mtp) cc_final: 0.7615 (mtp) REVERT: D 153 LEU cc_start: 0.7347 (tp) cc_final: 0.7006 (tp) REVERT: D 238 PHE cc_start: 0.5400 (m-80) cc_final: 0.4891 (m-80) REVERT: D 892 MET cc_start: 0.7034 (ptp) cc_final: 0.6498 (ptp) REVERT: A 682 TYR cc_start: 0.3865 (t80) cc_final: 0.3625 (t80) REVERT: A 892 MET cc_start: 0.9323 (tpp) cc_final: 0.9084 (mmm) REVERT: A 894 LEU cc_start: 0.8593 (mm) cc_final: 0.8365 (mm) REVERT: B 513 LEU cc_start: 0.7833 (tp) cc_final: 0.7592 (tp) REVERT: B 580 ASP cc_start: 0.7925 (m-30) cc_final: 0.7046 (m-30) REVERT: B 629 ILE cc_start: 0.8653 (tt) cc_final: 0.8428 (tt) REVERT: B 843 SER cc_start: 0.8581 (m) cc_final: 0.8241 (p) REVERT: B 867 MET cc_start: 0.7695 (ptp) cc_final: 0.7486 (ptp) REVERT: B 873 LEU cc_start: 0.8463 (mp) cc_final: 0.7151 (mt) REVERT: B 959 PHE cc_start: 0.7553 (t80) cc_final: 0.7274 (t80) REVERT: B 988 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6669 (tp-100) outliers start: 8 outliers final: 2 residues processed: 547 average time/residue: 0.4492 time to fit residues: 392.0938 Evaluate side-chains 385 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 381 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 30.0000 chunk 114 optimal weight: 30.0000 chunk 308 optimal weight: 10.0000 chunk 252 optimal weight: 40.0000 chunk 102 optimal weight: 50.0000 chunk 371 optimal weight: 7.9990 chunk 400 optimal weight: 30.0000 chunk 330 optimal weight: 40.0000 chunk 368 optimal weight: 40.0000 chunk 126 optimal weight: 4.9990 chunk 297 optimal weight: 6.9990 overall best weight: 11.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 HIS C 314 GLN C 555 ASN C1076 GLN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN B 45 GLN B 61 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 505 GLN B 563 HIS ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN B 645 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 997 HIS ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1086 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.761 32415 Z= 0.992 Angle : 1.134 31.943 43907 Z= 0.587 Chirality : 0.059 0.369 4900 Planarity : 0.009 0.103 5617 Dihedral : 9.177 150.913 4473 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 35.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.83 % Favored : 89.90 % Rotamer: Outliers : 0.30 % Allowed : 4.75 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.55 % Twisted General : 0.51 % 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: -3.13 (0.12), residues: 4066 helix: -1.45 (0.11), residues: 1630 sheet: -1.76 (0.22), residues: 478 loop : -2.71 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 276 HIS 0.019 0.003 HIS A1072 PHE 0.043 0.004 PHE B1033 TYR 0.058 0.004 TYR A 692 ARG 0.020 0.002 ARG C 662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 457 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 452 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 ASP cc_start: 0.7848 (m-30) cc_final: 0.7080 (t0) REVERT: C 895 MET cc_start: 0.8307 (mtp) cc_final: 0.7782 (mtp) REVERT: C 985 MET cc_start: 0.6956 (mtt) cc_final: 0.6579 (mtm) REVERT: C 1067 MET cc_start: 0.7529 (tpt) cc_final: 0.7274 (tpt) REVERT: D 919 ASP cc_start: 0.8571 (p0) cc_final: 0.8308 (p0) REVERT: D 990 LEU cc_start: 0.9529 (mm) cc_final: 0.9293 (mm) REVERT: D 1033 PHE cc_start: 0.7998 (t80) cc_final: 0.7699 (t80) REVERT: B 45 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.5721 (mm110) REVERT: B 580 ASP cc_start: 0.7776 (m-30) cc_final: 0.7088 (m-30) REVERT: B 698 MET cc_start: 0.5723 (mmt) cc_final: 0.4996 (tpp) REVERT: B 843 SER cc_start: 0.8602 (m) cc_final: 0.8130 (p) REVERT: B 867 MET cc_start: 0.8107 (ptp) cc_final: 0.7590 (ptp) REVERT: B 873 LEU cc_start: 0.8669 (mp) cc_final: 0.8058 (mt) REVERT: B 959 PHE cc_start: 0.8025 (t80) cc_final: 0.7732 (t80) REVERT: B 1029 ILE cc_start: 0.8522 (mm) cc_final: 0.8305 (mm) outliers start: 5 outliers final: 3 residues processed: 457 average time/residue: 0.4264 time to fit residues: 315.4715 Evaluate side-chains 314 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 310 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 8.9990 chunk 279 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 40.0000 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 372 optimal weight: 6.9990 chunk 394 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 ASN C1086 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 961 ASN ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN B 45 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5535 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.735 32415 Z= 0.880 Angle : 0.895 28.638 43907 Z= 0.461 Chirality : 0.052 0.337 4900 Planarity : 0.006 0.104 5617 Dihedral : 8.400 154.807 4473 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 26.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.65 % Favored : 91.08 % Rotamer: Outliers : 0.21 % Allowed : 2.64 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.33 % 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: -2.70 (0.12), residues: 4066 helix: -0.98 (0.12), residues: 1651 sheet: -1.56 (0.23), residues: 496 loop : -2.61 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 877 HIS 0.010 0.001 HIS A 545 PHE 0.027 0.002 PHE D 105 TYR 0.036 0.002 TYR C1073 ARG 0.011 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 460 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 458 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 540 LYS cc_start: 0.8530 (ptpp) cc_final: 0.8140 (ptpp) REVERT: C 579 TYR cc_start: 0.6229 (t80) cc_final: 0.5610 (t80) REVERT: C 704 TYR cc_start: 0.7462 (m-10) cc_final: 0.6851 (m-10) REVERT: C 892 MET cc_start: 0.7989 (ptp) cc_final: 0.7646 (ptp) REVERT: C 895 MET cc_start: 0.8052 (mtp) cc_final: 0.7463 (mtp) REVERT: C 1033 PHE cc_start: 0.8286 (t80) cc_final: 0.8073 (t80) REVERT: D 153 LEU cc_start: 0.7703 (tp) cc_final: 0.7463 (tp) REVERT: D 642 MET cc_start: 0.8676 (pmm) cc_final: 0.8186 (ptt) REVERT: D 990 LEU cc_start: 0.9543 (mm) cc_final: 0.9249 (mm) REVERT: D 1051 TYR cc_start: 0.8108 (m-80) cc_final: 0.7863 (m-80) REVERT: A 33 ARG cc_start: 0.4817 (pmt-80) cc_final: 0.4454 (ptt90) REVERT: A 560 MET cc_start: 0.4966 (mmm) cc_final: 0.4721 (mmm) REVERT: A 892 MET cc_start: 0.9245 (mmm) cc_final: 0.9009 (mmp) REVERT: A 1094 VAL cc_start: 0.7365 (m) cc_final: 0.6904 (m) REVERT: B 45 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.5706 (mm110) REVERT: B 580 ASP cc_start: 0.7837 (m-30) cc_final: 0.7049 (m-30) REVERT: B 698 MET cc_start: 0.4887 (mmt) cc_final: 0.4550 (mmt) REVERT: B 843 SER cc_start: 0.8681 (m) cc_final: 0.8415 (p) outliers start: 2 outliers final: 0 residues processed: 460 average time/residue: 0.4263 time to fit residues: 318.5642 Evaluate side-chains 325 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 7.9990 chunk 223 optimal weight: 40.0000 chunk 5 optimal weight: 0.0470 chunk 293 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 30.0000 chunk 272 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 0.9990 chunk 353 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 HIS ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 HIS ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.737 32415 Z= 0.869 Angle : 0.834 26.378 43907 Z= 0.428 Chirality : 0.052 0.372 4900 Planarity : 0.006 0.108 5617 Dihedral : 8.016 162.952 4473 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.97 % Favored : 90.81 % Rotamer: Outliers : 0.15 % Allowed : 1.99 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.31 % 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: -2.45 (0.12), residues: 4066 helix: -0.70 (0.12), residues: 1656 sheet: -1.41 (0.23), residues: 491 loop : -2.54 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 877 HIS 0.009 0.001 HIS A 545 PHE 0.029 0.002 PHE D 105 TYR 0.035 0.002 TYR A 692 ARG 0.031 0.001 ARG A 829 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 431 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 ASP cc_start: 0.7660 (m-30) cc_final: 0.7038 (t0) REVERT: C 556 MET cc_start: 0.6815 (mmm) cc_final: 0.6572 (mmm) REVERT: C 582 THR cc_start: 0.8684 (p) cc_final: 0.8463 (t) REVERT: C 892 MET cc_start: 0.7959 (ptp) cc_final: 0.7358 (ptp) REVERT: C 895 MET cc_start: 0.8129 (mtp) cc_final: 0.7261 (mtp) REVERT: C 1033 PHE cc_start: 0.8152 (t80) cc_final: 0.7292 (t80) REVERT: D 153 LEU cc_start: 0.7642 (tp) cc_final: 0.7427 (tp) REVERT: D 253 ILE cc_start: 0.7540 (mm) cc_final: 0.6912 (pt) REVERT: D 642 MET cc_start: 0.8697 (pmm) cc_final: 0.8196 (ptt) REVERT: D 678 THR cc_start: 0.8123 (m) cc_final: 0.6959 (m) REVERT: D 891 GLU cc_start: 0.7996 (mp0) cc_final: 0.7784 (mp0) REVERT: D 965 LYS cc_start: 0.8752 (pttt) cc_final: 0.7706 (tppt) REVERT: D 1033 PHE cc_start: 0.7425 (t80) cc_final: 0.7187 (t80) REVERT: D 1062 VAL cc_start: 0.9468 (t) cc_final: 0.9121 (p) REVERT: A 33 ARG cc_start: 0.4704 (pmt-80) cc_final: 0.4317 (ptt90) REVERT: A 510 GLN cc_start: 0.8290 (mt0) cc_final: 0.8008 (mt0) REVERT: A 560 MET cc_start: 0.4783 (mmm) cc_final: 0.4508 (mmm) REVERT: A 892 MET cc_start: 0.9240 (mmm) cc_final: 0.9020 (mmp) REVERT: A 933 ASP cc_start: 0.7065 (p0) cc_final: 0.6484 (t0) REVERT: B 580 ASP cc_start: 0.7761 (m-30) cc_final: 0.7099 (m-30) REVERT: B 698 MET cc_start: 0.4397 (mmt) cc_final: 0.4025 (mmt) REVERT: B 841 MET cc_start: 0.7935 (tpp) cc_final: 0.7723 (mmm) REVERT: B 1049 ASP cc_start: 0.7506 (p0) cc_final: 0.7298 (p0) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.4328 time to fit residues: 303.8261 Evaluate side-chains 314 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 3.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 20.0000 chunk 355 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 394 optimal weight: 7.9990 chunk 327 optimal weight: 50.0000 chunk 182 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN C 909 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 909 ASN ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 HIS ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN B1024 ASN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5572 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.735 32415 Z= 0.880 Angle : 0.830 25.448 43907 Z= 0.427 Chirality : 0.051 0.334 4900 Planarity : 0.006 0.107 5617 Dihedral : 7.951 172.603 4473 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.17 % Favored : 90.59 % Rotamer: Outliers : 0.15 % Allowed : 1.72 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.26 % 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: -2.34 (0.12), residues: 4066 helix: -0.57 (0.12), residues: 1657 sheet: -1.50 (0.23), residues: 508 loop : -2.48 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 877 HIS 0.010 0.001 HIS A1072 PHE 0.025 0.002 PHE D 105 TYR 0.029 0.002 TYR C1073 ARG 0.007 0.001 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 414 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 3.875 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: C 194 ASP cc_start: 0.7806 (m-30) cc_final: 0.7157 (t0) REVERT: C 556 MET cc_start: 0.6737 (mmm) cc_final: 0.6069 (mmm) REVERT: C 560 MET cc_start: 0.8266 (mpp) cc_final: 0.8040 (mpp) REVERT: C 608 LYS cc_start: 0.7692 (mttm) cc_final: 0.7340 (mtpp) REVERT: C 867 MET cc_start: 0.7847 (mmm) cc_final: 0.7543 (mmm) REVERT: C 1033 PHE cc_start: 0.7898 (t80) cc_final: 0.7666 (t80) REVERT: D 153 LEU cc_start: 0.7698 (tp) cc_final: 0.7476 (tp) REVERT: D 965 LYS cc_start: 0.8808 (pttt) cc_final: 0.7987 (tppt) REVERT: D 990 LEU cc_start: 0.9533 (mm) cc_final: 0.9256 (mm) REVERT: D 1033 PHE cc_start: 0.7601 (t80) cc_final: 0.7328 (t80) REVERT: A 33 ARG cc_start: 0.4751 (pmt-80) cc_final: 0.4300 (ptt90) REVERT: A 560 MET cc_start: 0.4804 (mmm) cc_final: 0.4535 (mmm) REVERT: A 892 MET cc_start: 0.9293 (mmm) cc_final: 0.9011 (mmp) REVERT: A 933 ASP cc_start: 0.7178 (p0) cc_final: 0.6449 (t0) REVERT: B 580 ASP cc_start: 0.7784 (m-30) cc_final: 0.7182 (m-30) REVERT: B 698 MET cc_start: 0.4309 (mmt) cc_final: 0.3977 (mmt) REVERT: B 843 SER cc_start: 0.8660 (m) cc_final: 0.8395 (p) REVERT: B 1049 ASP cc_start: 0.7588 (p0) cc_final: 0.7372 (p0) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.4118 time to fit residues: 283.0371 Evaluate side-chains 307 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 224 optimal weight: 50.0000 chunk 288 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 332 optimal weight: 50.0000 chunk 220 optimal weight: 30.0000 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 0.0670 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN C1098 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 HIS ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN B 981 ASN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.7092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.732 32415 Z= 0.866 Angle : 0.799 23.705 43907 Z= 0.410 Chirality : 0.051 0.326 4900 Planarity : 0.005 0.102 5617 Dihedral : 7.741 171.501 4473 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.07 % Favored : 90.66 % Rotamer: Outliers : 0.15 % Allowed : 1.13 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.31 % 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: -2.14 (0.13), residues: 4066 helix: -0.39 (0.12), residues: 1659 sheet: -1.38 (0.23), residues: 515 loop : -2.39 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 877 HIS 0.009 0.001 HIS A1072 PHE 0.022 0.002 PHE D1061 TYR 0.044 0.002 TYR C 579 ARG 0.019 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 422 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 3.616 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: C 608 LYS cc_start: 0.7750 (mttm) cc_final: 0.7361 (mtpp) REVERT: C 895 MET cc_start: 0.7810 (mtp) cc_final: 0.6991 (mtp) REVERT: C 1033 PHE cc_start: 0.7772 (t80) cc_final: 0.7448 (t80) REVERT: C 1063 LEU cc_start: 0.8753 (tp) cc_final: 0.8498 (tp) REVERT: D 678 THR cc_start: 0.8161 (m) cc_final: 0.7566 (m) REVERT: D 965 LYS cc_start: 0.8880 (pttt) cc_final: 0.8020 (tppt) REVERT: D 1033 PHE cc_start: 0.7497 (t80) cc_final: 0.7283 (t80) REVERT: D 1062 VAL cc_start: 0.9473 (t) cc_final: 0.9174 (p) REVERT: A 33 ARG cc_start: 0.4636 (pmt-80) cc_final: 0.4143 (ptt90) REVERT: A 560 MET cc_start: 0.4713 (mmm) cc_final: 0.4224 (mmm) REVERT: A 892 MET cc_start: 0.9306 (mmm) cc_final: 0.8996 (mmp) REVERT: A 933 ASP cc_start: 0.7049 (p0) cc_final: 0.6397 (t0) REVERT: B 19 ILE cc_start: 0.4905 (tp) cc_final: 0.4221 (tt) REVERT: B 566 VAL cc_start: 0.7488 (m) cc_final: 0.7245 (p) REVERT: B 580 ASP cc_start: 0.7896 (m-30) cc_final: 0.7147 (m-30) REVERT: B 860 THR cc_start: 0.8150 (p) cc_final: 0.7711 (t) REVERT: B 965 LYS cc_start: 0.9175 (tptp) cc_final: 0.8967 (tptp) REVERT: B 1049 ASP cc_start: 0.7575 (p0) cc_final: 0.7319 (p0) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.4165 time to fit residues: 287.4340 Evaluate side-chains 307 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 234 optimal weight: 50.0000 chunk 118 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 250 optimal weight: 50.0000 chunk 267 optimal weight: 7.9990 chunk 194 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 0.0270 overall best weight: 2.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN C1098 HIS D 47 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS D 671 ASN ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B 981 ASN B1076 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5510 moved from start: 0.7312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.732 32415 Z= 0.856 Angle : 0.771 22.710 43907 Z= 0.393 Chirality : 0.050 0.329 4900 Planarity : 0.005 0.099 5617 Dihedral : 7.456 151.468 4473 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.72 % Favored : 91.05 % Rotamer: Outliers : 0.15 % Allowed : 0.83 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.23 % 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: -1.94 (0.13), residues: 4066 helix: -0.23 (0.13), residues: 1661 sheet: -1.27 (0.23), residues: 512 loop : -2.28 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 877 HIS 0.008 0.001 HIS B 537 PHE 0.023 0.001 PHE D 347 TYR 0.027 0.002 TYR C 579 ARG 0.015 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 414 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 3.355 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: C 608 LYS cc_start: 0.7795 (mttm) cc_final: 0.7310 (mtpp) REVERT: C 867 MET cc_start: 0.7670 (tpp) cc_final: 0.7374 (tpp) REVERT: C 887 CYS cc_start: 0.8041 (m) cc_final: 0.7839 (m) REVERT: C 920 LEU cc_start: 0.8830 (tp) cc_final: 0.8537 (tp) REVERT: C 1063 LEU cc_start: 0.8713 (tp) cc_final: 0.8423 (tp) REVERT: D 278 MET cc_start: 0.4484 (tpp) cc_final: 0.3683 (tpt) REVERT: D 678 THR cc_start: 0.8188 (m) cc_final: 0.7054 (m) REVERT: A 33 ARG cc_start: 0.4446 (pmt-80) cc_final: 0.4022 (ptt90) REVERT: A 729 ARG cc_start: 0.5738 (ppt170) cc_final: 0.5073 (mmp80) REVERT: A 892 MET cc_start: 0.9186 (mmm) cc_final: 0.8952 (mmp) REVERT: A 933 ASP cc_start: 0.6969 (p0) cc_final: 0.6370 (t0) REVERT: A 963 MET cc_start: 0.9030 (tpp) cc_final: 0.8755 (mmm) REVERT: B 19 ILE cc_start: 0.4902 (tp) cc_final: 0.4124 (tt) REVERT: B 566 VAL cc_start: 0.7523 (m) cc_final: 0.7175 (p) REVERT: B 580 ASP cc_start: 0.7884 (m-30) cc_final: 0.7137 (m-30) REVERT: B 850 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6969 (tm-30) REVERT: B 965 LYS cc_start: 0.9172 (tptp) cc_final: 0.8959 (tptp) REVERT: B 1049 ASP cc_start: 0.7482 (p0) cc_final: 0.7168 (p0) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.4053 time to fit residues: 275.8534 Evaluate side-chains 305 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 5.9990 chunk 376 optimal weight: 8.9990 chunk 343 optimal weight: 50.0000 chunk 366 optimal weight: 0.9990 chunk 220 optimal weight: 0.4980 chunk 159 optimal weight: 20.0000 chunk 287 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 30.0000 chunk 346 optimal weight: 20.0000 chunk 365 optimal weight: 0.4980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 555 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 403 HIS ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN B 403 HIS ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.7582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.731 32415 Z= 0.859 Angle : 0.766 21.990 43907 Z= 0.392 Chirality : 0.049 0.325 4900 Planarity : 0.005 0.095 5617 Dihedral : 7.212 124.559 4473 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.62 % Favored : 91.15 % Rotamer: Outliers : 0.15 % Allowed : 0.48 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.26 % 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: -1.83 (0.13), residues: 4066 helix: -0.09 (0.13), residues: 1657 sheet: -1.20 (0.23), residues: 529 loop : -2.27 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 877 HIS 0.009 0.001 HIS B 537 PHE 0.031 0.002 PHE D1061 TYR 0.033 0.002 TYR A 213 ARG 0.012 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 400 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 3.503 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: C 608 LYS cc_start: 0.7673 (mttm) cc_final: 0.7279 (mtpp) REVERT: C 611 LYS cc_start: 0.8469 (ptmt) cc_final: 0.8188 (ttpp) REVERT: C 790 PHE cc_start: 0.5763 (t80) cc_final: 0.5493 (t80) REVERT: C 867 MET cc_start: 0.7570 (tpp) cc_final: 0.7313 (tpp) REVERT: C 887 CYS cc_start: 0.8081 (m) cc_final: 0.7824 (m) REVERT: C 1063 LEU cc_start: 0.8706 (tp) cc_final: 0.8452 (tp) REVERT: D 278 MET cc_start: 0.4433 (tpp) cc_final: 0.4139 (tpt) REVERT: D 642 MET cc_start: 0.8725 (pmm) cc_final: 0.8226 (ptt) REVERT: D 678 THR cc_start: 0.8240 (m) cc_final: 0.7217 (m) REVERT: D 1062 VAL cc_start: 0.9480 (t) cc_final: 0.9186 (p) REVERT: A 391 MET cc_start: -0.1463 (tpt) cc_final: -0.1734 (tpt) REVERT: A 729 ARG cc_start: 0.6112 (ppt170) cc_final: 0.5152 (mmt180) REVERT: A 892 MET cc_start: 0.9245 (mmm) cc_final: 0.8987 (mmp) REVERT: A 894 LEU cc_start: 0.8861 (mm) cc_final: 0.8651 (mm) REVERT: A 933 ASP cc_start: 0.7006 (p0) cc_final: 0.6381 (t0) REVERT: A 963 MET cc_start: 0.9013 (tpp) cc_final: 0.8762 (mmm) REVERT: B 19 ILE cc_start: 0.4886 (tp) cc_final: 0.3960 (tt) REVERT: B 355 LYS cc_start: 0.8448 (tptp) cc_final: 0.8216 (tptp) REVERT: B 504 MET cc_start: 0.6451 (mpp) cc_final: 0.3828 (ptt) REVERT: B 580 ASP cc_start: 0.7866 (m-30) cc_final: 0.7153 (m-30) REVERT: B 729 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.7112 (tmm160) REVERT: B 850 GLN cc_start: 0.7554 (mm-40) cc_final: 0.6969 (tm-30) REVERT: B 965 LYS cc_start: 0.9183 (tptp) cc_final: 0.8954 (tptp) REVERT: B 1049 ASP cc_start: 0.7491 (p0) cc_final: 0.7180 (p0) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.4234 time to fit residues: 280.6329 Evaluate side-chains 304 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 3.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 9.9990 chunk 387 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 183 optimal weight: 0.5980 chunk 269 optimal weight: 9.9990 chunk 406 optimal weight: 2.9990 chunk 374 optimal weight: 8.9990 chunk 323 optimal weight: 0.0470 chunk 33 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 198 optimal weight: 20.0000 overall best weight: 3.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.7760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.731 32415 Z= 0.857 Angle : 0.756 21.942 43907 Z= 0.386 Chirality : 0.049 0.319 4900 Planarity : 0.005 0.093 5617 Dihedral : 7.089 109.999 4473 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.48 % Favored : 91.35 % Rotamer: Outliers : 0.15 % Allowed : 0.18 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.21 % 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: -1.80 (0.13), residues: 4066 helix: -0.06 (0.13), residues: 1649 sheet: -1.13 (0.23), residues: 531 loop : -2.27 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 877 HIS 0.008 0.001 HIS A1072 PHE 0.032 0.002 PHE D1061 TYR 0.026 0.002 TYR C1073 ARG 0.012 0.001 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 399 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 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: C 608 LYS cc_start: 0.7702 (mttm) cc_final: 0.7299 (mtpp) REVERT: C 611 LYS cc_start: 0.8482 (ptmt) cc_final: 0.8222 (tmmt) REVERT: C 867 MET cc_start: 0.7444 (tpp) cc_final: 0.7241 (tpp) REVERT: C 1063 LEU cc_start: 0.8709 (tp) cc_final: 0.8488 (tp) REVERT: D 642 MET cc_start: 0.8711 (pmm) cc_final: 0.8213 (ptt) REVERT: D 678 THR cc_start: 0.8260 (m) cc_final: 0.7284 (m) REVERT: A 391 MET cc_start: -0.1497 (tpt) cc_final: -0.1870 (tpt) REVERT: A 666 MET cc_start: 0.1566 (ttt) cc_final: 0.1299 (tpp) REVERT: A 729 ARG cc_start: 0.6369 (ppt170) cc_final: 0.5281 (mmt180) REVERT: A 892 MET cc_start: 0.9262 (mmm) cc_final: 0.8960 (mmp) REVERT: A 933 ASP cc_start: 0.6939 (p0) cc_final: 0.6333 (t0) REVERT: A 963 MET cc_start: 0.9018 (tpp) cc_final: 0.8768 (mmm) REVERT: B 504 MET cc_start: 0.6546 (mpp) cc_final: 0.3860 (ptt) REVERT: B 580 ASP cc_start: 0.7865 (m-30) cc_final: 0.7150 (m-30) REVERT: B 850 GLN cc_start: 0.7550 (mm-40) cc_final: 0.6989 (tm-30) REVERT: B 928 LEU cc_start: 0.8591 (mt) cc_final: 0.8358 (mt) REVERT: B 1049 ASP cc_start: 0.7475 (p0) cc_final: 0.7168 (p0) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.4030 time to fit residues: 264.7713 Evaluate side-chains 302 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 0.1980 chunk 99 optimal weight: 0.3980 chunk 298 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 324 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS C 555 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.121777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.097114 restraints weight = 233545.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.099280 restraints weight = 221103.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.100727 restraints weight = 118036.248| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.7896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.731 32415 Z= 0.849 Angle : 0.748 21.904 43907 Z= 0.379 Chirality : 0.049 0.309 4900 Planarity : 0.005 0.094 5617 Dihedral : 6.918 103.701 4473 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.26 % Favored : 91.60 % Rotamer: Outliers : 0.12 % Allowed : 0.33 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 4066 helix: 0.02 (0.13), residues: 1659 sheet: -1.12 (0.23), residues: 530 loop : -2.18 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.002 TRP B 877 HIS 0.009 0.001 HIS B 537 PHE 0.028 0.001 PHE D1061 TYR 0.026 0.002 TYR C1073 ARG 0.011 0.000 ARG A 379 =============================================================================== Job complete usr+sys time: 7220.11 seconds wall clock time: 132 minutes 12.96 seconds (7932.96 seconds total)