Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 02:40:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j9e_9785/04_2023/6j9e_9785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j9e_9785/04_2023/6j9e_9785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j9e_9785/04_2023/6j9e_9785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j9e_9785/04_2023/6j9e_9785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j9e_9785/04_2023/6j9e_9785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j9e_9785/04_2023/6j9e_9785.pdb" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 61 5.49 5 Mg 1 5.21 5 S 74 5.16 5 C 15172 2.51 5 N 4344 2.21 5 O 4773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 190": "OD1" <-> "OD2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C ASP 309": "OD1" <-> "OD2" Residue "C ASP 321": "OD1" <-> "OD2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 608": "NH1" <-> "NH2" Residue "C PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 629": "OD1" <-> "OD2" Residue "C ASP 630": "OD1" <-> "OD2" Residue "C TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 677": "OE1" <-> "OE2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "C ARG 738": "NH1" <-> "NH2" Residue "C ARG 759": "NH1" <-> "NH2" Residue "C GLU 822": "OE1" <-> "OE2" Residue "C PHE 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 854": "OE1" <-> "OE2" Residue "C GLU 878": "OE1" <-> "OE2" Residue "C ASP 882": "OD1" <-> "OD2" Residue "C GLU 896": "OE1" <-> "OE2" Residue "C TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 905": "OE1" <-> "OE2" Residue "C GLU 928": "OE1" <-> "OE2" Residue "C ASP 954": "OD1" <-> "OD2" Residue "C ASP 959": "OD1" <-> "OD2" Residue "C ARG 965": "NH1" <-> "NH2" Residue "C ARG 973": "NH1" <-> "NH2" Residue "C GLU 981": "OE1" <-> "OE2" Residue "C GLU 1065": "OE1" <-> "OE2" Residue "C PHE 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1072": "OD1" <-> "OD2" Residue "C ASP 1082": "OD1" <-> "OD2" Residue "C PHE 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1230": "OD1" <-> "OD2" Residue "C TYR 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1265": "NH1" <-> "NH2" Residue "C ASP 1282": "OD1" <-> "OD2" Residue "C TYR 1293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1311": "NH1" <-> "NH2" Residue "C GLU 1380": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D GLU 407": "OE1" <-> "OE2" Residue "D ASP 410": "OD1" <-> "OD2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D GLU 586": "OE1" <-> "OE2" Residue "D TYR 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 635": "NH1" <-> "NH2" Residue "D ASP 643": "OD1" <-> "OD2" Residue "D ASP 649": "OD1" <-> "OD2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "D GLU 659": "OE1" <-> "OE2" Residue "D GLU 678": "OE1" <-> "OE2" Residue "D TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 685": "OD1" <-> "OD2" Residue "D ASP 700": "OD1" <-> "OD2" Residue "D ASP 716": "OD1" <-> "OD2" Residue "D ARG 750": "NH1" <-> "NH2" Residue "D ASP 752": "OD1" <-> "OD2" Residue "D GLU 766": "OE1" <-> "OE2" Residue "D ASP 803": "OD1" <-> "OD2" Residue "D GLU 891": "OE1" <-> "OE2" Residue "D PHE 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1145": "OD1" <-> "OD2" Residue "D ARG 1150": "NH1" <-> "NH2" Residue "D ASP 1154": "OD1" <-> "OD2" Residue "D TYR 1233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1237": "OE1" <-> "OE2" Residue "D ARG 1243": "NH1" <-> "NH2" Residue "D ASP 1304": "OD1" <-> "OD2" Residue "D ARG 1331": "NH1" <-> "NH2" Residue "D ARG 1356": "NH1" <-> "NH2" Residue "E ASP 8": "OD1" <-> "OD2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "J PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "J ASP 40": "OD1" <-> "OD2" Residue "J ASP 43": "OD1" <-> "OD2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 66": "OD1" <-> "OD2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 105": "OD1" <-> "OD2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F ASP 136": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 24427 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1543 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1449 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 108 Chain: "C" Number of atoms: 9355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1288, 9355 Classifications: {'peptide': 1288} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 51, 'TRANS': 1236} Chain breaks: 9 Unresolved non-hydrogen bonds: 803 Unresolved non-hydrogen angles: 966 Unresolved non-hydrogen dihedrals: 656 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 16, 'ASN:plan1': 5, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 52, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 530 Chain: "D" Number of atoms: 8733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1200, 8733 Classifications: {'peptide': 1200} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 45, 'TRANS': 1154} Chain breaks: 8 Unresolved non-hydrogen bonds: 686 Unresolved non-hydrogen angles: 824 Unresolved non-hydrogen dihedrals: 578 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 4, 'GLU:plan': 32, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 435 Chain: "E" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 467 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 582 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 266 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "J" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 488 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1091 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 161 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12897 SG CYS D 72 109.827 59.692 50.244 1.00 95.66 S ATOM 12987 SG CYS D 85 112.589 59.900 52.648 1.00 93.10 S ATOM 18397 SG CYS D 815 84.743 75.812 115.744 1.00 55.06 S ATOM 18833 SG CYS D 890 84.722 77.733 111.566 1.00 62.92 S ATOM 18898 SG CYS D 900 81.466 76.712 114.314 1.00 45.45 S Time building chain proxies: 13.44, per 1000 atoms: 0.55 Number of scatterers: 24427 At special positions: 0 Unit cell: (138.918, 165.282, 150.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 74 16.00 P 61 15.00 Mg 1 11.99 O 4773 8.00 N 4344 7.00 C 15172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.89 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 900 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 890 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 815 " 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5946 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 45 sheets defined 38.8% alpha, 14.7% beta 24 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 7.13 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.594A pdb=" N LEU A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.541A pdb=" N VAL A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 227 removed outlier: 3.852A pdb=" N VAL A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.894A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 211 through 230 removed outlier: 3.930A pdb=" N PHE B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.790A pdb=" N ARG C 11 " --> pdb=" O THR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 41 removed outlier: 3.848A pdb=" N VAL C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 removed outlier: 3.635A pdb=" N ALA C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.502A pdb=" N GLY C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.511A pdb=" N ARG C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C 254 " --> pdb=" O ARG C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 254' Processing helix chain 'C' and resid 278 through 287 Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 351 through 360 removed outlier: 3.604A pdb=" N ASN C 355 " --> pdb=" O PRO C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 377 Processing helix chain 'C' and resid 383 through 396 removed outlier: 4.076A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 416 Processing helix chain 'C' and resid 437 through 448 removed outlier: 3.867A pdb=" N LYS C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 448 " --> pdb=" O VAL C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 466 Processing helix chain 'C' and resid 483 through 507 removed outlier: 3.621A pdb=" N MET C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 505 " --> pdb=" O ARG C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 520 removed outlier: 3.679A pdb=" N GLU C 519 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 536 removed outlier: 4.768A pdb=" N VAL C 526 " --> pdb=" O ASN C 522 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 536 " --> pdb=" O GLU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 572 through 577 removed outlier: 3.834A pdb=" N ASP C 577 " --> pdb=" O PHE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 583 removed outlier: 3.634A pdb=" N TYR C 583 " --> pdb=" O PRO C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 688 removed outlier: 4.264A pdb=" N THR C 688 " --> pdb=" O PRO C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 702 removed outlier: 3.514A pdb=" N HIS C 701 " --> pdb=" O PHE C 698 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 702 " --> pdb=" O LEU C 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 698 through 702' Processing helix chain 'C' and resid 703 through 714 removed outlier: 3.587A pdb=" N ASN C 712 " --> pdb=" O LEU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 717 No H-bonds generated for 'chain 'C' and resid 715 through 717' Processing helix chain 'C' and resid 732 through 741 removed outlier: 4.369A pdb=" N GLY C 741 " --> pdb=" O ALA C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 854 removed outlier: 3.870A pdb=" N GLU C 854 " --> pdb=" O ARG C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'C' and resid 926 through 935 Processing helix chain 'C' and resid 971 through 1008 Processing helix chain 'C' and resid 1053 through 1078 Processing helix chain 'C' and resid 1122 through 1126 Processing helix chain 'C' and resid 1142 through 1148 removed outlier: 4.031A pdb=" N SER C1146 " --> pdb=" O LEU C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1150 through 1175 removed outlier: 3.666A pdb=" N LEU C1154 " --> pdb=" O ILE C1150 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1191 removed outlier: 3.754A pdb=" N LEU C1182 " --> pdb=" O ALA C1178 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN C1191 " --> pdb=" O ASP C1187 " (cutoff:3.500A) Processing helix chain 'C' and resid 1208 through 1218 Processing helix chain 'C' and resid 1233 through 1244 removed outlier: 4.311A pdb=" N ALA C1244 " --> pdb=" O MET C1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 1280 through 1285 removed outlier: 3.979A pdb=" N LYS C1284 " --> pdb=" O LEU C1280 " (cutoff:3.500A) Processing helix chain 'C' and resid 1304 through 1308 removed outlier: 4.002A pdb=" N PHE C1307 " --> pdb=" O LYS C1304 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C1308 " --> pdb=" O ALA C1305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1304 through 1308' Processing helix chain 'C' and resid 1313 through 1323 Processing helix chain 'C' and resid 1325 through 1334 removed outlier: 3.633A pdb=" N LEU C1333 " --> pdb=" O LEU C1329 " (cutoff:3.500A) Processing helix chain 'C' and resid 1339 through 1353 removed outlier: 3.636A pdb=" N ARG C1343 " --> pdb=" O ASP C1339 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN C1344 " --> pdb=" O VAL C1340 " (cutoff:3.500A) Processing helix chain 'C' and resid 1362 through 1374 removed outlier: 3.679A pdb=" N ASN C1366 " --> pdb=" O PRO C1362 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 removed outlier: 3.705A pdb=" N PHE D 8 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN D 9 " --> pdb=" O ASN D 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 5 through 9' Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.778A pdb=" N VAL D 97 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D 98 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.620A pdb=" N ILE D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.700A pdb=" N VAL D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.605A pdb=" N ALA D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.521A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.897A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 484 removed outlier: 3.552A pdb=" N MET D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 515 removed outlier: 3.552A pdb=" N GLY D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 575 through 581 Processing helix chain 'D' and resid 598 through 613 Processing helix chain 'D' and resid 615 through 635 removed outlier: 3.646A pdb=" N ARG D 635 " --> pdb=" O ALA D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 671 removed outlier: 4.161A pdb=" N LYS D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 704 removed outlier: 3.524A pdb=" N ARG D 679 " --> pdb=" O THR D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 730 removed outlier: 4.237A pdb=" N GLY D 730 " --> pdb=" O MET D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 769 through 805 removed outlier: 3.619A pdb=" N ASN D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 867 through 878 Processing helix chain 'D' and resid 897 through 902 removed outlier: 3.543A pdb=" N TYR D 901 " --> pdb=" O CYS D 897 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY D 902 " --> pdb=" O ALA D 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 897 through 902' Processing helix chain 'D' and resid 918 through 926 Processing helix chain 'D' and resid 927 through 931 removed outlier: 4.213A pdb=" N THR D 930 " --> pdb=" O GLU D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1149 Processing helix chain 'D' and resid 1217 through 1225 removed outlier: 3.659A pdb=" N ILE D1221 " --> pdb=" O SER D1217 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D1225 " --> pdb=" O ILE D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1227 through 1246 Processing helix chain 'D' and resid 1250 through 1262 removed outlier: 4.490A pdb=" N ILE D1254 " --> pdb=" O ASN D1250 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1294 removed outlier: 4.538A pdb=" N VAL D1294 " --> pdb=" O ASN D1290 " (cutoff:3.500A) Processing helix chain 'D' and resid 1309 through 1314 removed outlier: 4.213A pdb=" N SER D1314 " --> pdb=" O ILE D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1328 through 1340 Processing helix chain 'D' and resid 1348 through 1355 Processing helix chain 'D' and resid 1363 through 1371 removed outlier: 3.528A pdb=" N ARG D1371 " --> pdb=" O HIS D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 13 removed outlier: 3.744A pdb=" N VAL E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.668A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 61 through 76 Processing helix chain 'J' and resid 46 through 61 removed outlier: 3.665A pdb=" N PHE J 50 " --> pdb=" O SER J 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 10 removed outlier: 3.664A pdb=" N LEU F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 39 Processing helix chain 'F' and resid 107 through 136 Processing helix chain 'F' and resid 205 through 212 removed outlier: 3.529A pdb=" N MET F 209 " --> pdb=" O ALA F 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 6.745A pdb=" N ASP A 198 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 183 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 181 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 61 removed outlier: 5.276A pdb=" N PHE A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY A 148 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE A 56 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU A 146 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 58 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 104 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 101 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.968A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.512A pdb=" N GLN A 152 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 174 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 17 removed outlier: 3.901A pdb=" N ARG B 181 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 61 removed outlier: 5.499A pdb=" N PHE B 54 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY B 148 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE B 56 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU B 146 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU B 58 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 144 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.882A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 152 removed outlier: 3.526A pdb=" N ALA B 174 " --> pdb=" O GLN B 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 14 through 15 removed outlier: 6.836A pdb=" N LYS C 14 " --> pdb=" O ALA C1225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 80 removed outlier: 3.788A pdb=" N ALA C 72 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C 76 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N THR C 104 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR C 78 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG C 102 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU C 80 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA C 99 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU C 131 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 101 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 105 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN C 125 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU C 107 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LYS C 123 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE C 109 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR C 121 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.686A pdb=" N PHE C 141 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 149 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 541 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 479 through 482 removed outlier: 6.025A pdb=" N SER C 152 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 159 through 165 removed outlier: 4.048A pdb=" N LEU C 176 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 202 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 235 through 236 Processing sheet with id=AB7, first strand: chain 'C' and resid 307 through 308 removed outlier: 3.728A pdb=" N VAL C 307 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 317 " --> pdb=" O VAL C 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 586 through 587 removed outlier: 4.561A pdb=" N SER C 602 " --> pdb=" O CYS C 587 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 608 through 609 removed outlier: 5.328A pdb=" N ASP C 630 " --> pdb=" O LYS C 621 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 608 through 609 removed outlier: 3.740A pdb=" N LYS C 673 " --> pdb=" O VAL C 662 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 744 through 745 removed outlier: 7.122A pdb=" N VAL C 744 " --> pdb=" O LEU C 812 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 750 through 755 removed outlier: 5.988A pdb=" N ILE C 752 " --> pdb=" O LYS C 763 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LYS C 763 " --> pdb=" O ILE C 752 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN C 754 " --> pdb=" O VAL C 761 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 786 through 787 removed outlier: 4.028A pdb=" N THR C 786 " --> pdb=" O ILE C 794 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 794 " --> pdb=" O THR C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 1137 through 1139 removed outlier: 8.835A pdb=" N ILE C1137 " --> pdb=" O ASN C 828 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU C 830 " --> pdb=" O ILE C1137 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU C1139 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA C 832 " --> pdb=" O LEU C1139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET C 829 " --> pdb=" O MET C1272 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C1270 " --> pdb=" O ILE C 831 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE C 833 " --> pdb=" O THR C1268 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N THR C1268 " --> pdb=" O PHE C 833 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 844 through 847 removed outlier: 7.930A pdb=" N ILE C 845 " --> pdb=" O SER C1118 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C1120 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU C 847 " --> pdb=" O VAL C1120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 859 through 870 removed outlier: 3.932A pdb=" N LYS C1089 " --> pdb=" O ALA C 869 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 959 " --> pdb=" O PHE C1094 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA C1096 " --> pdb=" O VAL C 957 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL C 957 " --> pdb=" O ALA C1096 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 911 through 913 removed outlier: 3.839A pdb=" N VAL C 913 " --> pdb=" O LEU C 947 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 916 through 917 Processing sheet with id=AD1, first strand: chain 'C' and resid 1286 through 1288 removed outlier: 3.662A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1286 through 1288 removed outlier: 8.019A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1310 through 1312 Processing sheet with id=AD4, first strand: chain 'C' and resid 1377 through 1381 Processing sheet with id=AD5, first strand: chain 'D' and resid 104 through 112 removed outlier: 10.404A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.626A pdb=" N LEU D 160 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 547 through 556 Processing sheet with id=AD8, first strand: chain 'D' and resid 707 through 710 Processing sheet with id=AD9, first strand: chain 'D' and resid 821 through 823 removed outlier: 4.034A pdb=" N VAL D 882 " --> pdb=" O MET D 823 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 826 through 827 removed outlier: 7.029A pdb=" N ILE D 826 " --> pdb=" O VAL D 833 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 952 through 953 removed outlier: 3.945A pdb=" N ALA D1020 " --> pdb=" O ILE D 952 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 959 through 960 removed outlier: 3.827A pdb=" N GLY D 982 " --> pdb=" O LEU D 999 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1187 through 1192 removed outlier: 4.026A pdb=" N HIS D1187 " --> pdb=" O ILE D1179 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D1179 " --> pdb=" O HIS D1187 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D1177 " --> pdb=" O GLU D1189 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1278 through 1280 Processing sheet with id=AE6, first strand: chain 'J' and resid 14 through 17 removed outlier: 6.519A pdb=" N LEU J 22 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP J 38 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL J 24 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU J 36 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL J 26 " --> pdb=" O LEU J 34 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 48 through 49 removed outlier: 4.203A pdb=" N GLU F 58 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 61 " --> pdb=" O GLN F 100 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN F 100 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 145 through 150 removed outlier: 6.588A pdb=" N PHE F 155 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA F 149 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 190 through 191 removed outlier: 4.629A pdb=" N ARG F 191 " --> pdb=" O GLN F 198 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN F 198 " --> pdb=" O ARG F 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 985 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 11.02 Time building geometry restraints manager: 9.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7110 1.33 - 1.45: 3742 1.45 - 1.57: 13804 1.57 - 1.69: 120 1.69 - 1.81: 129 Bond restraints: 24905 Sorted by residual: bond pdb=" C GLU D 927 " pdb=" N PRO D 928 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.85e+00 bond pdb=" C3' DA H 14 " pdb=" O3' DA H 14 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" C3' DG G 12 " pdb=" O3' DG G 12 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.43e+00 bond pdb=" C ASP J 47 " pdb=" N PRO J 48 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.25e-02 6.40e+03 2.28e+00 bond pdb=" C PHE C 62 " pdb=" N PRO C 63 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.10e+00 ... (remaining 24900 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.10: 857 106.10 - 113.12: 13800 113.12 - 120.15: 8662 120.15 - 127.17: 10559 127.17 - 134.20: 292 Bond angle restraints: 34170 Sorted by residual: angle pdb=" C VAL C 61 " pdb=" N PHE C 62 " pdb=" CA PHE C 62 " ideal model delta sigma weight residual 120.06 124.82 -4.76 1.19e+00 7.06e-01 1.60e+01 angle pdb=" C GLY C 69 " pdb=" N ASN C 70 " pdb=" CA ASN C 70 " ideal model delta sigma weight residual 122.07 127.33 -5.26 1.43e+00 4.89e-01 1.35e+01 angle pdb=" N PHE C 62 " pdb=" CA PHE C 62 " pdb=" C PHE C 62 " ideal model delta sigma weight residual 113.57 118.22 -4.65 1.38e+00 5.25e-01 1.14e+01 angle pdb=" C PHE D 377 " pdb=" N LYS D 378 " pdb=" CA LYS D 378 " ideal model delta sigma weight residual 120.09 124.22 -4.13 1.25e+00 6.40e-01 1.09e+01 angle pdb=" C ALA C1305 " pdb=" N GLN C1306 " pdb=" CA GLN C1306 " ideal model delta sigma weight residual 122.61 127.71 -5.10 1.56e+00 4.11e-01 1.07e+01 ... (remaining 34165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.94: 14148 27.94 - 55.88: 551 55.88 - 83.82: 62 83.82 - 111.75: 4 111.75 - 139.69: 2 Dihedral angle restraints: 14767 sinusoidal: 5568 harmonic: 9199 Sorted by residual: dihedral pdb=" CA ALA D 426 " pdb=" C ALA D 426 " pdb=" N PRO D 427 " pdb=" CA PRO D 427 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA GLY C1324 " pdb=" C GLY C1324 " pdb=" N ALA C1325 " pdb=" CA ALA C1325 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 14764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3171 0.045 - 0.091: 659 0.091 - 0.136: 263 0.136 - 0.181: 28 0.181 - 0.226: 2 Chirality restraints: 4123 Sorted by residual: chirality pdb=" CB ILE C 752 " pdb=" CA ILE C 752 " pdb=" CG1 ILE C 752 " pdb=" CG2 ILE C 752 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE C 820 " pdb=" CA ILE C 820 " pdb=" CG1 ILE C 820 " pdb=" CG2 ILE C 820 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE C 323 " pdb=" CA ILE C 323 " pdb=" CG1 ILE C 323 " pdb=" CG2 ILE C 323 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 4120 not shown) Planarity restraints: 4249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 62 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO C 63 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 63 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 63 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 426 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO D 427 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D1140 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO D1141 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D1141 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D1141 " -0.030 5.00e-02 4.00e+02 ... (remaining 4246 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1465 2.74 - 3.28: 21756 3.28 - 3.82: 38485 3.82 - 4.36: 42934 4.36 - 4.90: 75567 Nonbonded interactions: 180207 Sorted by model distance: nonbonded pdb=" O3' A I 20 " pdb="MG MG D1501 " model vdw 2.198 2.170 nonbonded pdb=" O SER J 20 " pdb=" OG SER J 20 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR C1323 " pdb=" O ILE D 434 " model vdw 2.314 2.440 nonbonded pdb=" OG SER D1217 " pdb=" OD1 ASP D1220 " model vdw 2.324 2.440 nonbonded pdb=" OD1 ASP D 464 " pdb=" O2' A I 20 " model vdw 2.325 2.440 ... (remaining 180202 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 11 through 19 or (resid 20 through 21 and (name N or name \ CA or name C or name O or name CB )) or resid 22 through 28 or (resid 29 and (na \ me N or name CA or name C or name O or name CB )) or resid 30 through 61 or (res \ id 62 and (name N or name CA or name C or name O or name CB )) or resid 63 or (r \ esid 64 through 72 and (name N or name CA or name C or name O or name CB )) or r \ esid 73 or (resid 74 through 76 and (name N or name CA or name C or name O or na \ me CB )) or resid 77 through 81 or (resid 82 and (name N or name CA or name C or \ name O or name CB )) or resid 83 through 86 or (resid 87 and (name N or name CA \ or name C or name O or name CB )) or resid 88 through 91 or (resid 92 and (name \ N or name CA or name C or name O or name CB )) or resid 93 through 100 or (resi \ d 101 and (name N or name CA or name C or name O or name CB )) or resid 102 thro \ ugh 103 or (resid 104 through 105 and (name N or name CA or name C or name O or \ name CB )) or resid 106 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 138 or (resid 139 through 141 an \ d (name N or name CA or name C or name O or name CB )) or resid 142 through 155 \ or resid 170 through 204 or (resid 205 and (name N or name CA or name C or name \ O or name CB )) or resid 206 through 212 or (resid 213 through 215 and (name N o \ r name CA or name C or name O or name CB )) or resid 216 through 230)) selection = (chain 'B' and (resid 11 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 113 or (resid 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 or (resid 116 and (name N \ or name CA or name C or name O or name CB )) or resid 117 through 145 or (resid \ 146 and (name N or name CA or name C or name O or name CB )) or resid 147 throug \ h 194 or (resid 195 through 196 and (name N or name CA or name C or name O or na \ me CB )) or resid 197 through 230)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.640 Check model and map are aligned: 0.380 Set scattering table: 0.200 Process input model: 73.400 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.003 0.049 24905 Z= 0.180 Angle : 0.613 10.790 34170 Z= 0.340 Chirality : 0.044 0.226 4123 Planarity : 0.005 0.065 4249 Dihedral : 14.311 139.692 8821 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.11), residues: 3143 helix: -2.73 (0.10), residues: 1136 sheet: -0.77 (0.26), residues: 363 loop : -2.73 (0.12), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 532 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 533 average time/residue: 0.4755 time to fit residues: 361.5324 Evaluate side-chains 358 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 357 time to evaluate : 2.694 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2109 time to fit residues: 4.1412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 0.0040 chunk 244 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 153 optimal weight: 0.0010 chunk 187 optimal weight: 8.9990 chunk 292 optimal weight: 0.8980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 389 ASN C 393 ASN C 475 HIS C 490 ASN C 579 HIS C 992 GLN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1205 GLN C1344 ASN C1349 ASN D 170 GLN D 340 GLN D 458 ASN D 880 GLN D1260 GLN J 6 GLN J 17 GLN F 103 ASN F 128 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 24905 Z= 0.162 Angle : 0.481 8.966 34170 Z= 0.252 Chirality : 0.039 0.140 4123 Planarity : 0.004 0.048 4249 Dihedral : 12.239 138.396 4062 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 3143 helix: -0.11 (0.14), residues: 1129 sheet: -0.33 (0.26), residues: 392 loop : -2.22 (0.13), residues: 1622 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 374 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 392 average time/residue: 0.3981 time to fit residues: 237.9429 Evaluate side-chains 370 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 348 time to evaluate : 2.651 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2234 time to fit residues: 12.8513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 243 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 292 optimal weight: 0.5980 chunk 316 optimal weight: 20.0000 chunk 260 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 478 ASN C1111 HIS C1310 GLN D 458 ASN D 666 GLN D1367 HIS ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 24905 Z= 0.345 Angle : 0.591 9.182 34170 Z= 0.307 Chirality : 0.043 0.178 4123 Planarity : 0.004 0.046 4249 Dihedral : 12.514 138.071 4062 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3143 helix: 0.76 (0.15), residues: 1137 sheet: -0.21 (0.27), residues: 375 loop : -1.93 (0.13), residues: 1631 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 360 time to evaluate : 2.731 Fit side-chains outliers start: 61 outliers final: 38 residues processed: 407 average time/residue: 0.3888 time to fit residues: 244.4263 Evaluate side-chains 368 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 330 time to evaluate : 2.748 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2152 time to fit residues: 19.2127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 0.0050 chunk 220 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 311 optimal weight: 10.0000 chunk 153 optimal weight: 0.4980 chunk 278 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS C 478 ASN C1149 ASN D 435 GLN D 458 ASN D 489 ASN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 24905 Z= 0.197 Angle : 0.496 9.832 34170 Z= 0.257 Chirality : 0.040 0.164 4123 Planarity : 0.003 0.039 4249 Dihedral : 12.461 141.952 4062 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3143 helix: 1.37 (0.16), residues: 1139 sheet: -0.12 (0.26), residues: 394 loop : -1.72 (0.14), residues: 1610 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 342 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 18 residues processed: 375 average time/residue: 0.3966 time to fit residues: 228.6659 Evaluate side-chains 339 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 321 time to evaluate : 3.383 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2322 time to fit residues: 11.4576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 7.9990 chunk 176 optimal weight: 0.0040 chunk 4 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS C1060 GLN C1191 ASN D 266 ASN D 386 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 24905 Z= 0.157 Angle : 0.471 9.156 34170 Z= 0.243 Chirality : 0.039 0.147 4123 Planarity : 0.003 0.036 4249 Dihedral : 12.413 143.434 4062 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3143 helix: 1.74 (0.16), residues: 1142 sheet: 0.02 (0.26), residues: 400 loop : -1.53 (0.15), residues: 1601 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 337 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 356 average time/residue: 0.3916 time to fit residues: 214.2185 Evaluate side-chains 337 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 321 time to evaluate : 2.607 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2572 time to fit residues: 10.8984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 311 optimal weight: 0.0000 chunk 258 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 386 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 24905 Z= 0.197 Angle : 0.493 11.824 34170 Z= 0.253 Chirality : 0.040 0.151 4123 Planarity : 0.003 0.041 4249 Dihedral : 12.446 143.802 4062 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3143 helix: 1.90 (0.16), residues: 1136 sheet: 0.08 (0.26), residues: 401 loop : -1.44 (0.15), residues: 1606 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 330 time to evaluate : 2.732 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 353 average time/residue: 0.3859 time to fit residues: 211.4495 Evaluate side-chains 335 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 316 time to evaluate : 2.700 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2185 time to fit residues: 11.6859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 262 optimal weight: 0.0980 chunk 173 optimal weight: 3.9990 chunk 310 optimal weight: 0.5980 chunk 194 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24905 Z= 0.195 Angle : 0.496 11.772 34170 Z= 0.254 Chirality : 0.040 0.202 4123 Planarity : 0.003 0.039 4249 Dihedral : 12.467 144.679 4062 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3143 helix: 2.01 (0.16), residues: 1135 sheet: 0.15 (0.26), residues: 399 loop : -1.37 (0.15), residues: 1609 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 328 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 347 average time/residue: 0.3983 time to fit residues: 213.6234 Evaluate side-chains 326 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 316 time to evaluate : 2.864 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2461 time to fit residues: 8.5413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 243 optimal weight: 0.0570 chunk 282 optimal weight: 3.9990 overall best weight: 1.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 ASN C1079 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 24905 Z= 0.304 Angle : 0.578 13.376 34170 Z= 0.298 Chirality : 0.042 0.295 4123 Planarity : 0.004 0.038 4249 Dihedral : 12.670 141.168 4062 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3143 helix: 1.76 (0.16), residues: 1135 sheet: -0.10 (0.26), residues: 386 loop : -1.37 (0.15), residues: 1622 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 321 time to evaluate : 2.838 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 22 residues processed: 345 average time/residue: 0.4060 time to fit residues: 217.6638 Evaluate side-chains 331 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 309 time to evaluate : 2.922 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2313 time to fit residues: 13.5638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 8.9990 chunk 271 optimal weight: 0.6980 chunk 289 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 261 optimal weight: 0.0770 chunk 273 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1192 HIS ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 24905 Z= 0.153 Angle : 0.503 12.484 34170 Z= 0.259 Chirality : 0.040 0.264 4123 Planarity : 0.003 0.039 4249 Dihedral : 12.571 147.596 4062 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3143 helix: 2.02 (0.16), residues: 1142 sheet: 0.11 (0.26), residues: 386 loop : -1.29 (0.15), residues: 1615 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 324 time to evaluate : 2.771 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 328 average time/residue: 0.3820 time to fit residues: 196.2140 Evaluate side-chains 317 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 313 time to evaluate : 2.714 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2464 time to fit residues: 5.4930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 320 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 24905 Z= 0.275 Angle : 0.566 13.655 34170 Z= 0.289 Chirality : 0.042 0.271 4123 Planarity : 0.004 0.042 4249 Dihedral : 12.624 143.346 4062 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3143 helix: 1.95 (0.16), residues: 1130 sheet: -0.04 (0.26), residues: 375 loop : -1.30 (0.15), residues: 1638 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 316 time to evaluate : 3.504 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 321 average time/residue: 0.3985 time to fit residues: 199.8485 Evaluate side-chains 310 residues out of total 2707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 305 time to evaluate : 3.041 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2283 time to fit residues: 6.1630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 224 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111384 restraints weight = 36391.489| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.24 r_work: 0.3165 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 24905 Z= 0.231 Angle : 0.544 13.874 34170 Z= 0.277 Chirality : 0.041 0.264 4123 Planarity : 0.004 0.040 4249 Dihedral : 12.627 145.218 4062 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3143 helix: 1.94 (0.16), residues: 1141 sheet: 0.04 (0.26), residues: 377 loop : -1.28 (0.15), residues: 1625 =============================================================================== Job complete usr+sys time: 5501.28 seconds wall clock time: 99 minutes 22.77 seconds (5962.77 seconds total)