Starting phenix.real_space_refine (version: 1.21rc1) on Sun May 14 00:13:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/05_2023/6psw_20466_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/05_2023/6psw_20466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/05_2023/6psw_20466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/05_2023/6psw_20466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/05_2023/6psw_20466_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/05_2023/6psw_20466_trim_updated.pdb" } resolution = 3.7 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 124 5.49 5 Mg 1 5.21 5 S 136 5.16 5 C 20127 2.51 5 N 5780 2.21 5 O 6524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 136": "OE1" <-> "OE2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 14": "OD1" <-> "OD2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 33": "OD1" <-> "OD2" Residue "I GLU 40": "OE1" <-> "OE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 158": "OD1" <-> "OD2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 231": "OE1" <-> "OE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ASP 281": "OD1" <-> "OD2" Residue "I GLU 290": "OE1" <-> "OE2" Residue "I TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 374": "OE1" <-> "OE2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I ASP 423": "OD1" <-> "OD2" Residue "I ASP 427": "OD1" <-> "OD2" Residue "I ASP 434": "OD1" <-> "OD2" Residue "I ASP 446": "OD1" <-> "OD2" Residue "I ASP 516": "OD1" <-> "OD2" Residue "I ASP 549": "OD1" <-> "OD2" Residue "I TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 601": "OD1" <-> "OD2" Residue "I TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 632": "OD1" <-> "OD2" Residue "I GLU 641": "OE1" <-> "OE2" Residue "I ASP 696": "OD1" <-> "OD2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I ASP 781": "OD1" <-> "OD2" Residue "I ASP 785": "OD1" <-> "OD2" Residue "I PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I ASP 826": "OD1" <-> "OD2" Residue "I ASP 853": "OD1" <-> "OD2" Residue "I ASP 912": "OD1" <-> "OD2" Residue "I ASP 937": "OD1" <-> "OD2" Residue "I ARG 974": "NH1" <-> "NH2" Residue "I GLU 987": "OE1" <-> "OE2" Residue "I ARG 1156": "NH1" <-> "NH2" Residue "I PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1296": "OD1" <-> "OD2" Residue "I TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1341": "OD1" <-> "OD2" Residue "J ASP 18": "OD1" <-> "OD2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 177": "OD1" <-> "OD2" Residue "J ASP 248": "OD1" <-> "OD2" Residue "J ASP 289": "OD1" <-> "OD2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J ASP 304": "OD1" <-> "OD2" Residue "J ASP 329": "OD1" <-> "OD2" Residue "J PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J ASP 462": "OD1" <-> "OD2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "J PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 731": "NH1" <-> "NH2" Residue "J ARG 738": "NH1" <-> "NH2" Residue "J ARG 799": "NH1" <-> "NH2" Residue "J ASP 802": "OD1" <-> "OD2" Residue "J ASP 812": "OD1" <-> "OD2" Residue "J ASP 837": "OD1" <-> "OD2" Residue "J GLU 846": "OE1" <-> "OE2" Residue "J PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 981": "OE1" <-> "OE2" Residue "J GLU 987": "OE1" <-> "OE2" Residue "J TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1052": "OE1" <-> "OE2" Residue "J ASP 1073": "OD1" <-> "OD2" Residue "J ASP 1111": "OD1" <-> "OD2" Residue "J GLU 1146": "OE1" <-> "OE2" Residue "J GLU 1158": "OE1" <-> "OE2" Residue "J GLU 1188": "OE1" <-> "OE2" Residue "J PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K ARG 3": "NH1" <-> "NH2" Residue "K ASP 8": "OD1" <-> "OD2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K ARG 67": "NH1" <-> "NH2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "L ARG 113": "NH1" <-> "NH2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "L ASP 118": "OD1" <-> "OD2" Residue "L PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 278": "OD1" <-> "OD2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L ASP 332": "OD1" <-> "OD2" Residue "L GLU 349": "OE1" <-> "OE2" Residue "L TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 417": "OD1" <-> "OD2" Residue "L ARG 441": "NH1" <-> "NH2" Residue "L GLU 481": "OE1" <-> "OE2" Residue "L ARG 584": "NH1" <-> "NH2" Residue "L ASP 612": "OD1" <-> "OD2" Residue "L ASP 613": "OD1" <-> "OD2" Residue "M ASP 250": "OD1" <-> "OD2" Residue "M ASP 258": "OD1" <-> "OD2" Residue "M GLU 261": "OE1" <-> "OE2" Residue "M ASP 280": "OD1" <-> "OD2" Residue "M GLU 286": "OE1" <-> "OE2" Residue "M GLU 319": "OE1" <-> "OE2" Residue "N GLU 4": "OE1" <-> "OE2" Residue "N TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 66": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 32695 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1762 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10571 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1284} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 10460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10460 Classifications: {'peptide': 1345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1288} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3854 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 14, 'TRANS': 458} Chain breaks: 2 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 66} Chain: "O" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1270 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain: "P" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1272 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14460 SG CYS J 70 76.872 99.753 110.158 1.00 33.15 S ATOM 14474 SG CYS J 72 77.146 102.675 111.995 1.00 38.61 S ATOM 14582 SG CYS J 85 74.415 101.147 113.335 1.00 42.93 S ATOM 14606 SG CYS J 88 73.523 100.283 110.077 1.00 47.24 S ATOM 20288 SG CYS J 814 73.930 38.981 83.279 1.00 26.40 S ATOM 20853 SG CYS J 888 73.547 42.857 82.747 1.00 23.18 S ATOM 20925 SG CYS J 898 75.066 40.229 80.222 1.00 16.65 S ATOM 29825 SG CYS N 40 53.649 54.250 22.072 1.00 73.58 S ATOM 29984 SG CYS N 61 56.367 55.850 24.356 1.00 81.89 S Time building chain proxies: 17.28, per 1000 atoms: 0.53 Number of scatterers: 32695 At special positions: 0 Unit cell: (163.8, 156, 166.4, 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 3 29.99 S 136 16.00 P 124 15.00 Mg 1 11.99 O 6524 8.00 N 5780 7.00 C 20127 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: 15.58 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " Number of angles added : 6 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 33 sheets defined 36.9% alpha, 8.9% beta 48 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 12.67 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 removed outlier: 3.736A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 156 through 159 Processing helix chain 'G' and resid 162 through 164 No H-bonds generated for 'chain 'G' and resid 162 through 164' Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'H' and resid 35 through 49 removed outlier: 3.609A pdb=" N LEU H 39 " --> pdb=" O PHE H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 87 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 228 removed outlier: 4.218A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 8 No H-bonds generated for 'chain 'I' and resid 5 through 8' Processing helix chain 'I' and resid 29 through 39 removed outlier: 4.112A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 56 removed outlier: 3.655A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 319 through 328 removed outlier: 3.626A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 388 Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 436 Processing helix chain 'I' and resid 456 through 480 removed outlier: 4.314A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 541 through 543 No H-bonds generated for 'chain 'I' and resid 541 through 543' Processing helix chain 'I' and resid 609 through 612 No H-bonds generated for 'chain 'I' and resid 609 through 612' Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 688 removed outlier: 3.639A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 821 through 824 No H-bonds generated for 'chain 'I' and resid 821 through 824' Processing helix chain 'I' and resid 861 through 863 No H-bonds generated for 'chain 'I' and resid 861 through 863' Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 943 through 980 removed outlier: 4.380A pdb=" N ALA I 977 " --> pdb=" O SER I 973 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL I 980 " --> pdb=" O ARG I 976 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1101 through 1105 removed outlier: 3.881A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1105' Processing helix chain 'I' and resid 1109 through 1133 removed outlier: 3.609A pdb=" N LEU I1117 " --> pdb=" O GLU I1114 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1148 Processing helix chain 'I' and resid 1168 through 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1242 No H-bonds generated for 'chain 'I' and resid 1239 through 1242' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1285 through 1291 Processing helix chain 'I' and resid 1300 through 1309 removed outlier: 3.955A pdb=" N TYR I1305 " --> pdb=" O ARG I1301 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE I1308 " --> pdb=" O MET I1304 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1330 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 115 through 118 No H-bonds generated for 'chain 'J' and resid 115 through 118' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 removed outlier: 3.884A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 191 removed outlier: 4.108A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 264 through 285 removed outlier: 3.525A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 4.054A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 453 through 457 Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 4.073A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 592 Processing helix chain 'J' and resid 599 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 641 through 643 No H-bonds generated for 'chain 'J' and resid 641 through 643' Processing helix chain 'J' and resid 649 through 669 Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 769 through 789 removed outlier: 4.016A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) Processing helix chain 'J' and resid 791 through 803 removed outlier: 3.940A pdb=" N LEU J 796 " --> pdb=" O ASN J 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 866 through 875 removed outlier: 3.675A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 928 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1138 through 1146 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1244 Processing helix chain 'J' and resid 1250 through 1262 removed outlier: 3.528A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG J1262 " --> pdb=" O ARG J1258 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1292 Processing helix chain 'J' and resid 1309 through 1313 Processing helix chain 'J' and resid 1319 through 1324 removed outlier: 3.792A pdb=" N SER J1324 " --> pdb=" O ILE J1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 1328 through 1338 removed outlier: 3.658A pdb=" N ALA J1336 " --> pdb=" O LEU J1332 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL J1337 " --> pdb=" O THR J1333 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1352 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 3.703A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 13 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 removed outlier: 3.626A pdb=" N GLU K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.724A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 106 Processing helix chain 'L' and resid 115 through 135 Processing helix chain 'L' and resid 138 through 153 Processing helix chain 'L' and resid 158 through 161 No H-bonds generated for 'chain 'L' and resid 158 through 161' Processing helix chain 'L' and resid 216 through 232 Processing helix chain 'L' and resid 245 through 256 Processing helix chain 'L' and resid 263 through 289 Processing helix chain 'L' and resid 299 through 306 Processing helix chain 'L' and resid 317 through 320 No H-bonds generated for 'chain 'L' and resid 317 through 320' Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 355 through 394 removed outlier: 4.046A pdb=" N ASN L 362 " --> pdb=" O VAL L 358 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU L 378 " --> pdb=" O ARG L 374 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR L 394 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 Processing helix chain 'L' and resid 427 through 445 removed outlier: 4.250A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 474 removed outlier: 4.925A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 486 No H-bonds generated for 'chain 'L' and resid 483 through 486' Processing helix chain 'L' and resid 493 through 500 Processing helix chain 'L' and resid 512 through 514 No H-bonds generated for 'chain 'L' and resid 512 through 514' Processing helix chain 'L' and resid 519 through 522 Processing helix chain 'L' and resid 531 through 550 removed outlier: 3.572A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 579 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'L' and resid 605 through 610 Processing helix chain 'M' and resid 257 through 259 No H-bonds generated for 'chain 'M' and resid 257 through 259' Processing helix chain 'M' and resid 264 through 272 Processing helix chain 'M' and resid 278 through 281 No H-bonds generated for 'chain 'M' and resid 278 through 281' Processing helix chain 'M' and resid 286 through 290 Processing helix chain 'M' and resid 297 through 310 Processing helix chain 'N' and resid 5 through 26 Processing helix chain 'N' and resid 46 through 51 Processing helix chain 'N' and resid 59 through 69 Processing sheet with id= A, first strand: chain 'G' and resid 24 through 28 removed outlier: 3.868A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.552A pdb=" N VAL G 146 " --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.685A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 23 through 28 removed outlier: 3.777A pdb=" N ALA H 184 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 99 through 105 removed outlier: 3.663A pdb=" N MET H 142 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 58 through 60 removed outlier: 7.105A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.533A pdb=" N ILE I 127 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= I, first strand: chain 'I' and resid 149 through 151 Processing sheet with id= J, first strand: chain 'I' and resid 154 through 157 Processing sheet with id= K, first strand: chain 'I' and resid 228 through 231 Processing sheet with id= L, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= M, first strand: chain 'I' and resid 603 through 606 Processing sheet with id= N, first strand: chain 'I' and resid 633 through 636 Processing sheet with id= O, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.637A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.462A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 834 through 840 removed outlier: 3.520A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= S, first strand: chain 'I' and resid 255 through 257 removed outlier: 5.619A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 301 through 303 removed outlier: 5.339A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 19 through 21 Processing sheet with id= V, first strand: chain 'J' and resid 104 through 106 Processing sheet with id= W, first strand: chain 'J' and resid 252 through 254 Processing sheet with id= X, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= Y, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= Z, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= AA, first strand: chain 'J' and resid 959 through 961 Processing sheet with id= AB, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AC, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id= AD, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 4.493A pdb=" N ALA J1097 " --> pdb=" O ILE J1080 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 1046 through 1051 Processing sheet with id= AF, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AG, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.085A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 2958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 13.60 Time building geometry restraints manager: 16.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10748 1.34 - 1.46: 7481 1.46 - 1.59: 14726 1.59 - 1.72: 251 1.72 - 1.84: 239 Bond restraints: 33445 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.842 -0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.731 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.712 -0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.694 -0.152 2.00e-02 2.50e+03 5.76e+01 ... (remaining 33440 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.17: 1029 105.17 - 112.42: 17804 112.42 - 119.68: 11236 119.68 - 126.93: 15068 126.93 - 134.19: 572 Bond angle restraints: 45709 Sorted by residual: angle pdb=" N ILE N 27 " pdb=" CA ILE N 27 " pdb=" C ILE N 27 " ideal model delta sigma weight residual 106.21 113.68 -7.47 1.07e+00 8.73e-01 4.87e+01 angle pdb=" C THR L 94 " pdb=" N THR L 95 " pdb=" CA THR L 95 " ideal model delta sigma weight residual 122.56 113.32 9.24 1.50e+00 4.44e-01 3.79e+01 angle pdb=" N ILE J 490 " pdb=" CA ILE J 490 " pdb=" C ILE J 490 " ideal model delta sigma weight residual 113.20 108.82 4.38 9.60e-01 1.09e+00 2.08e+01 angle pdb=" N LEU I 237 " pdb=" CA LEU I 237 " pdb=" C LEU I 237 " ideal model delta sigma weight residual 110.91 116.10 -5.19 1.17e+00 7.31e-01 1.97e+01 angle pdb=" N ILE I1109 " pdb=" CA ILE I1109 " pdb=" C ILE I1109 " ideal model delta sigma weight residual 113.07 107.45 5.62 1.36e+00 5.41e-01 1.71e+01 ... (remaining 45704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 18965 32.36 - 64.71: 1072 64.71 - 97.07: 78 97.07 - 129.42: 5 129.42 - 161.78: 3 Dihedral angle restraints: 20123 sinusoidal: 9086 harmonic: 11037 Sorted by residual: dihedral pdb=" CA PHE I 545 " pdb=" C PHE I 545 " pdb=" N GLU I 546 " pdb=" CA GLU I 546 " ideal model delta harmonic sigma weight residual -180.00 -127.47 -52.53 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA PHE I 57 " pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CA PRO I 58 " ideal model delta harmonic sigma weight residual 180.00 139.27 40.73 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA VAL I 442 " pdb=" C VAL I 442 " pdb=" N ASP I 443 " pdb=" CA ASP I 443 " ideal model delta harmonic sigma weight residual -180.00 -145.49 -34.51 0 5.00e+00 4.00e-02 4.76e+01 ... (remaining 20120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4241 0.060 - 0.119: 896 0.119 - 0.179: 77 0.179 - 0.239: 7 0.239 - 0.298: 3 Chirality restraints: 5224 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.83 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASP I 516 " pdb=" N ASP I 516 " pdb=" C ASP I 516 " pdb=" CB ASP I 516 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 5221 not shown) Planarity restraints: 5525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG I 974 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C ARG I 974 " 0.063 2.00e-02 2.50e+03 pdb=" O ARG I 974 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE I 975 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 375 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C ALA L 375 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA L 375 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS L 376 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET H 51 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO H 52 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 52 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 52 " 0.041 5.00e-02 4.00e+02 ... (remaining 5522 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 391 2.57 - 3.15: 30279 3.15 - 3.73: 51571 3.73 - 4.32: 73436 4.32 - 4.90: 116059 Nonbonded interactions: 271736 Sorted by model distance: nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 1.987 2.170 nonbonded pdb=" OH TYR I 346 " pdb=" OD1 ASN I 437 " model vdw 2.023 2.440 nonbonded pdb=" OG1 THR I 216 " pdb=" OE1 GLN I 219 " model vdw 2.026 2.440 nonbonded pdb=" O ASN J 962 " pdb=" OG1 THR J 980 " model vdw 2.059 2.440 nonbonded pdb=" OH TYR I 179 " pdb=" OE2 GLU I 458 " model vdw 2.063 2.440 ... (remaining 271731 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 'G' and ((resid 6 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 158 or resid 171 through 233 or (resid 234 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 6 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 121 or (resid 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 228 or (resid 229 through 230 and \ (name N or name CA or name C or name O or name CB )) or resid 231 through 232 o \ r (resid 233 through 234 and (name N or name CA or name C or name O or name CB ) \ ))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 6.940 Check model and map are aligned: 0.500 Set scattering table: 0.280 Process input model: 96.020 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.110 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.008 0.310 33445 Z= 0.508 Angle : 0.887 9.961 45709 Z= 0.518 Chirality : 0.047 0.298 5224 Planarity : 0.005 0.075 5525 Dihedral : 18.686 161.776 13005 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 42.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.43 % Favored : 88.38 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.11), residues: 3805 helix: -1.94 (0.11), residues: 1474 sheet: -3.31 (0.21), residues: 382 loop : -3.18 (0.12), residues: 1949 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 597 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 609 average time/residue: 0.5261 time to fit residues: 486.3167 Evaluate side-chains 373 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 364 time to evaluate : 3.633 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3037 time to fit residues: 9.9595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 4.9990 chunk 296 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 chunk 355 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 128 HIS I 20 GLN ** I 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 832 HIS I 834 GLN ** I 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN I1116 HIS I1135 GLN I1220 GLN J 157 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN J 465 GLN ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN J 594 GLN J 680 ASN J 720 ASN J 817 HIS J 910 ASN J 951 GLN J 954 ASN J1023 HIS J1249 ASN K 15 ASN L 227 GLN L 242 HIS L 271 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 GLN L 600 HIS N 30 HIS N 68 GLN N 71 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 33445 Z= 0.208 Angle : 0.660 9.173 45709 Z= 0.346 Chirality : 0.044 0.305 5224 Planarity : 0.005 0.077 5525 Dihedral : 18.429 160.565 5439 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.54 % Favored : 92.38 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.12), residues: 3805 helix: -0.63 (0.13), residues: 1468 sheet: -2.68 (0.23), residues: 367 loop : -2.60 (0.13), residues: 1970 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 504 time to evaluate : 3.738 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 outliers start: 84 outliers final: 41 residues processed: 559 average time/residue: 0.4702 time to fit residues: 416.1932 Evaluate side-chains 420 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 379 time to evaluate : 3.654 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2986 time to fit residues: 27.9174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 295 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 97 optimal weight: 0.0070 chunk 355 optimal weight: 6.9990 chunk 384 optimal weight: 10.0000 chunk 316 optimal weight: 0.2980 chunk 352 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 285 optimal weight: 8.9990 overall best weight: 2.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 93 GLN I 20 GLN I 69 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN J 489 ASN J1108 GLN J1249 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 33445 Z= 0.275 Angle : 0.661 10.955 45709 Z= 0.345 Chirality : 0.044 0.258 5224 Planarity : 0.005 0.088 5525 Dihedral : 18.269 157.977 5439 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.33 % Favored : 91.59 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 3805 helix: -0.20 (0.13), residues: 1468 sheet: -2.23 (0.24), residues: 364 loop : -2.35 (0.13), residues: 1973 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 416 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 46 residues processed: 487 average time/residue: 0.4587 time to fit residues: 359.7785 Evaluate side-chains 412 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 366 time to evaluate : 3.960 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3164 time to fit residues: 32.3950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 351 optimal weight: 0.0050 chunk 267 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 39 optimal weight: 0.2980 chunk 169 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 356 optimal weight: 0.2980 chunk 377 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS I 582 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN J 594 GLN J1279 GLN J1366 HIS ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 33445 Z= 0.205 Angle : 0.612 10.294 45709 Z= 0.320 Chirality : 0.042 0.236 5224 Planarity : 0.004 0.074 5525 Dihedral : 18.053 157.452 5439 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.10 % Favored : 92.83 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.13), residues: 3805 helix: 0.14 (0.13), residues: 1469 sheet: -1.86 (0.25), residues: 374 loop : -2.16 (0.13), residues: 1962 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 414 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 33 residues processed: 467 average time/residue: 0.4577 time to fit residues: 347.4064 Evaluate side-chains 393 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 360 time to evaluate : 3.756 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3084 time to fit residues: 24.0357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 314 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 281 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 322 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 0.0020 chunk 339 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS G 147 GLN ** I 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1072 ASN J 158 GLN J 594 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 33445 Z= 0.203 Angle : 0.598 9.670 45709 Z= 0.313 Chirality : 0.042 0.207 5224 Planarity : 0.004 0.071 5525 Dihedral : 17.908 155.546 5439 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.39 % Favored : 92.54 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3805 helix: 0.33 (0.14), residues: 1476 sheet: -1.60 (0.25), residues: 379 loop : -2.01 (0.14), residues: 1950 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 393 time to evaluate : 3.869 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 23 residues processed: 430 average time/residue: 0.4574 time to fit residues: 322.4522 Evaluate side-chains 374 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 351 time to evaluate : 3.557 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3203 time to fit residues: 18.3121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 1.9990 chunk 340 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 314 optimal weight: 0.0870 chunk 175 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 0.0770 chunk 198 optimal weight: 6.9990 overall best weight: 2.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS G 147 GLN ** I 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 33445 Z= 0.291 Angle : 0.643 9.951 45709 Z= 0.336 Chirality : 0.043 0.235 5224 Planarity : 0.005 0.095 5525 Dihedral : 17.946 151.859 5439 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.20 % Favored : 91.72 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.13), residues: 3805 helix: 0.35 (0.14), residues: 1465 sheet: -1.56 (0.26), residues: 382 loop : -1.88 (0.14), residues: 1958 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 363 time to evaluate : 4.214 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 25 residues processed: 392 average time/residue: 0.4519 time to fit residues: 289.4975 Evaluate side-chains 357 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 332 time to evaluate : 3.640 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3660 time to fit residues: 21.1210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 364 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 276 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 376 optimal weight: 0.3980 chunk 235 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS ** I 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 HIS ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 33445 Z= 0.171 Angle : 0.585 12.115 45709 Z= 0.304 Chirality : 0.041 0.209 5224 Planarity : 0.004 0.070 5525 Dihedral : 17.646 152.426 5439 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3805 helix: 0.54 (0.14), residues: 1471 sheet: -1.44 (0.26), residues: 390 loop : -1.86 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 400 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 421 average time/residue: 0.4629 time to fit residues: 320.6591 Evaluate side-chains 363 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 348 time to evaluate : 4.022 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3250 time to fit residues: 15.0477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7817 > 50: distance: 67 - 70: 21.365 distance: 70 - 71: 29.190 distance: 71 - 72: 17.030 distance: 71 - 74: 11.927 distance: 72 - 73: 27.759 distance: 72 - 78: 31.072 distance: 74 - 75: 33.046 distance: 75 - 76: 6.387 distance: 75 - 77: 10.449 distance: 78 - 79: 27.895 distance: 79 - 80: 29.623 distance: 80 - 81: 12.055 distance: 80 - 82: 32.500 distance: 82 - 83: 18.916 distance: 83 - 84: 10.894 distance: 83 - 86: 28.851 distance: 84 - 85: 23.677 distance: 84 - 91: 11.984 distance: 86 - 87: 10.166 distance: 87 - 88: 8.315 distance: 88 - 89: 36.973 distance: 88 - 90: 13.155 distance: 91 - 92: 15.867 distance: 91 - 97: 15.621 distance: 92 - 93: 10.679 distance: 92 - 95: 12.393 distance: 93 - 94: 14.641 distance: 93 - 98: 8.208 distance: 95 - 96: 6.416 distance: 96 - 97: 24.358 distance: 98 - 99: 19.155 distance: 99 - 100: 6.922 distance: 99 - 102: 6.275 distance: 100 - 101: 34.438 distance: 100 - 106: 19.444 distance: 102 - 103: 15.617 distance: 102 - 104: 19.923 distance: 103 - 105: 13.002 distance: 106 - 107: 16.921 distance: 107 - 108: 18.214 distance: 107 - 110: 12.657 distance: 108 - 109: 21.558 distance: 108 - 114: 38.225 distance: 110 - 111: 8.674 distance: 110 - 112: 6.860 distance: 111 - 113: 16.603 distance: 114 - 115: 17.563 distance: 115 - 116: 37.314 distance: 115 - 118: 9.717 distance: 116 - 117: 27.956 distance: 116 - 121: 51.902 distance: 118 - 119: 34.452 distance: 118 - 120: 45.412 distance: 121 - 122: 19.717 distance: 122 - 123: 31.031 distance: 122 - 125: 13.092 distance: 123 - 124: 37.558 distance: 123 - 128: 20.798 distance: 125 - 126: 9.409 distance: 126 - 127: 26.965 distance: 128 - 129: 23.121 distance: 129 - 130: 28.201 distance: 129 - 132: 27.044 distance: 130 - 131: 17.593 distance: 130 - 134: 14.523 distance: 132 - 133: 21.878 distance: 134 - 135: 19.334 distance: 135 - 136: 25.148 distance: 135 - 138: 19.203 distance: 136 - 137: 15.887 distance: 136 - 143: 24.756 distance: 138 - 139: 15.591 distance: 139 - 140: 15.063 distance: 140 - 141: 7.340 distance: 140 - 142: 23.487