Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 16:44:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2023/7mke_23893_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2023/7mke_23893.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/7mke_23893/04_2023/7mke_23893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2023/7mke_23893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2023/7mke_23893_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2023/7mke_23893_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= 0.014 sd= 0.070 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 79 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 18989 2.51 5 N 5413 2.21 5 O 6029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 226": "OE1" <-> "OE2" Residue "I ASP 254": "OD1" <-> "OD2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 516": "OD1" <-> "OD2" Residue "I TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I GLU 898": "OE1" <-> "OE2" Residue "I GLU 968": "OE1" <-> "OE2" Residue "I PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 1147": "NH1" <-> "NH2" Residue "I PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1192": "OE1" <-> "OE2" Residue "I TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1274": "OE1" <-> "OE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 532": "OE1" <-> "OE2" Residue "J GLU 556": "OE1" <-> "OE2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 811": "OE1" <-> "OE2" Residue "J PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1143": "OD1" <-> "OD2" Residue "J PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1200": "OE1" <-> "OE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "J PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1317": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "L PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 481": "OE1" <-> "OE2" Residue "L GLU 491": "OE1" <-> "OE2" 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: 30641 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1808 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "J" Number of atoms: 10377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10377 Classifications: {'peptide': 1335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1278} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3781 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 451} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 907 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "Q" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 749 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" 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} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14538 SG CYS J 70 100.691 52.642 74.134 1.00 96.23 S ATOM 14552 SG CYS J 72 99.702 50.812 72.593 1.00 96.96 S ATOM 14660 SG CYS J 85 102.572 51.997 70.782 1.00103.27 S ATOM 14684 SG CYS J 88 101.419 54.865 72.505 1.00104.22 S ATOM 20367 SG CYS J 814 124.499 107.404 109.180 1.00 80.68 S ATOM 20932 SG CYS J 888 121.489 105.813 107.397 1.00 74.16 S ATOM 20983 SG CYS J 895 122.663 104.491 110.686 1.00 68.11 S ATOM 21004 SG CYS J 898 121.210 107.972 110.653 1.00 69.90 S Time building chain proxies: 15.22, per 1000 atoms: 0.50 Number of scatterers: 30641 At special positions: 0 Unit cell: (152.64, 182.32, 193.98, 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 128 16.00 P 79 15.00 Mg 1 11.99 O 6029 8.00 N 5413 7.00 C 18989 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: 15.81 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 85 " 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 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " Number of angles added : 12 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 129 helices and 36 sheets defined 36.8% alpha, 9.0% beta 37 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 11.63 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 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 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 232 removed outlier: 3.718A pdb=" N GLU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 Processing helix chain 'H' and resid 78 through 86 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 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 213 through 228 removed outlier: 3.718A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 207 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 removed outlier: 3.558A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 289 through 294 removed outlier: 3.823A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 289 through 294' Processing helix chain 'I' and resid 319 through 327 Processing helix chain 'I' and resid 346 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 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.690A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 removed outlier: 4.878A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 540 through 542 No H-bonds generated for 'chain 'I' and resid 540 through 542' Processing helix chain 'I' and resid 545 through 548 No H-bonds generated for 'chain 'I' and resid 545 through 548' Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 610 through 613 No H-bonds generated for 'chain 'I' and resid 610 through 613' Processing helix chain 'I' and resid 664 through 667 removed outlier: 3.802A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 667' 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: 4.478A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) removed outlier: 4.631A 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 820 through 824 Processing helix chain 'I' and resid 861 through 864 removed outlier: 3.713A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 861 through 864' Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 943 through 980 removed outlier: 3.650A pdb=" N VAL I 980 " --> pdb=" O ARG I 976 " (cutoff:3.500A) Processing helix chain 'I' and resid 987 through 991 removed outlier: 3.686A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 987 through 991' Processing helix chain 'I' and resid 997 through 999 No H-bonds generated for 'chain 'I' and resid 997 through 999' Processing helix chain 'I' and resid 1008 through 1037 removed outlier: 3.927A pdb=" N GLU I1012 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN I1013 " --> pdb=" O ASN I1009 " (cutoff:3.500A) Processing helix chain 'I' and resid 1100 through 1106 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1150 Processing helix chain 'I' and resid 1168 through 1176 Processing helix chain 'I' and resid 1192 through 1201 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 Processing helix chain 'I' and resid 1321 through 1332 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 96 through 99 removed outlier: 3.541A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 96 through 99' Processing helix chain 'J' and resid 114 through 118 Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 191 Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 235 through 237 No H-bonds generated for 'chain 'J' and resid 235 through 237' Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 264 through 285 Processing helix chain 'J' and resid 289 through 300 Processing helix chain 'J' and resid 304 through 308 Processing helix chain 'J' and resid 327 through 331 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: 3.738A pdb=" N TRP J 409 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP J 410 " --> pdb=" O VAL J 407 " (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 451 through 453 No H-bonds generated for 'chain 'J' and resid 451 through 453' 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 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 581 removed outlier: 4.127A 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 650 through 669 Processing helix chain 'J' and resid 675 through 701 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 769 through 803 removed outlier: 4.313A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 837 No H-bonds generated for 'chain 'J' and resid 835 through 837' Processing helix chain 'J' and resid 866 through 873 Processing helix chain 'J' and resid 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 915 through 929 Proline residue: J 926 - end of helix removed outlier: 5.639A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 4.251A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1312 No H-bonds generated for 'chain 'J' and resid 1309 through 1312' Processing helix chain 'J' and resid 1320 through 1323 No H-bonds generated for 'chain 'J' and resid 1320 through 1323' Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1348 through 1352 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 3.876A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 61 through 79 removed outlier: 4.078A pdb=" N GLU K 79 " --> pdb=" O GLN K 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 107 removed outlier: 3.870A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 136 removed outlier: 3.742A pdb=" N GLU L 136 " --> pdb=" O CYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 152 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 233 Processing helix chain 'L' and resid 245 through 257 Processing helix chain 'L' and resid 263 through 291 removed outlier: 4.138A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 306 removed outlier: 3.783A pdb=" N THR L 304 " --> pdb=" O LYS L 300 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 322 No H-bonds generated for 'chain 'L' and resid 320 through 322' Processing helix chain 'L' and resid 325 through 332 removed outlier: 3.857A pdb=" N LYS L 329 " --> pdb=" O PRO L 325 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS L 331 " --> pdb=" O SER L 327 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP L 332 " --> pdb=" O GLU L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 351 removed outlier: 3.535A pdb=" N THR L 351 " --> pdb=" O ILE L 347 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 393 removed outlier: 5.729A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 417 Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 445 Processing helix chain 'L' and resid 454 through 474 removed outlier: 3.806A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 486 Processing helix chain 'L' and resid 493 through 500 Processing helix chain 'L' and resid 519 through 522 No H-bonds generated for 'chain 'L' and resid 519 through 522' Processing helix chain 'L' and resid 531 through 549 Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 580 Processing helix chain 'L' and resid 584 through 598 Processing helix chain 'L' and resid 604 through 610 removed outlier: 4.148A pdb=" N PHE L 610 " --> pdb=" O VAL L 606 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 23 through 28 removed outlier: 3.817A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'G' and resid 98 through 105 Processing sheet with id= D, first strand: chain 'G' and resid 188 through 190 removed outlier: 4.120A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.541A pdb=" N GLY G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 24 through 28 Processing sheet with id= G, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.789A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 188 through 190 Processing sheet with id= I, first strand: chain 'H' and resid 109 through 111 Processing sheet with id= J, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= K, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= L, first strand: chain 'I' and resid 148 through 151 removed outlier: 3.593A pdb=" N HIS I 150 " --> pdb=" O ARG I 452 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 154 through 156 Processing sheet with id= N, first strand: chain 'I' and resid 185 through 188 removed outlier: 3.737A pdb=" N GLU I 187 " --> pdb=" O PHE I 195 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= P, first strand: chain 'I' and resid 633 through 635 Processing sheet with id= Q, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.686A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 1227 through 1232 removed outlier: 6.328A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 830 through 839 removed outlier: 3.946A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= U, first strand: chain 'I' and resid 66 through 75 removed outlier: 7.043A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.865A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 301 through 303 removed outlier: 5.413A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 589 through 594 removed outlier: 5.637A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.804A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.642A pdb=" N ARG J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AB, first strand: chain 'J' and resid 547 through 549 Processing sheet with id= AC, first strand: chain 'J' and resid 552 through 556 Processing sheet with id= AD, first strand: chain 'J' and resid 820 through 823 removed outlier: 3.630A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.520A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AG, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AH, first strand: chain 'J' and resid 1172 through 1174 Processing sheet with id= AI, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.512A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.735A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 182 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 13.14 Time building geometry restraints manager: 14.19 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: 9847 1.34 - 1.46: 5954 1.46 - 1.58: 15063 1.58 - 1.70: 171 1.70 - 1.82: 234 Bond restraints: 31269 Sorted by residual: bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C19 1N7 L 702 " pdb=" C3 1N7 L 702 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.818 -0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C3 1N7 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.729 -0.197 2.00e-02 2.50e+03 9.68e+01 ... (remaining 31264 not shown) Histogram of bond angle deviations from ideal: 97.30 - 105.63: 965 105.63 - 113.97: 18664 113.97 - 122.31: 18087 122.31 - 130.64: 4756 130.64 - 138.98: 111 Bond angle restraints: 42583 Sorted by residual: angle pdb=" C LEU I 487 " pdb=" N MET I 488 " pdb=" CA MET I 488 " ideal model delta sigma weight residual 120.67 138.98 -18.31 1.34e+00 5.57e-01 1.87e+02 angle pdb=" C ILE H 168 " pdb=" N GLY H 169 " pdb=" CA GLY H 169 " ideal model delta sigma weight residual 121.70 132.49 -10.79 1.80e+00 3.09e-01 3.59e+01 angle pdb=" C LEU I 484 " pdb=" N ASP I 485 " pdb=" CA ASP I 485 " ideal model delta sigma weight residual 121.70 131.01 -9.31 1.80e+00 3.09e-01 2.68e+01 angle pdb=" N ASP I 516 " pdb=" CA ASP I 516 " pdb=" C ASP I 516 " ideal model delta sigma weight residual 109.96 102.78 7.18 1.49e+00 4.50e-01 2.32e+01 angle pdb=" C LEU I 397 " pdb=" N SER I 398 " pdb=" CA SER I 398 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 ... (remaining 42578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 18069 34.44 - 68.88: 807 68.88 - 103.31: 35 103.31 - 137.75: 1 137.75 - 172.19: 3 Dihedral angle restraints: 18915 sinusoidal: 8338 harmonic: 10577 Sorted by residual: dihedral pdb=" CA PRO I 897 " pdb=" C PRO I 897 " pdb=" N GLU I 898 " pdb=" CA GLU I 898 " ideal model delta harmonic sigma weight residual -180.00 -138.69 -41.31 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -140.53 -39.47 0 5.00e+00 4.00e-02 6.23e+01 dihedral pdb=" CA ARG G 235 " pdb=" C ARG G 235 " pdb=" N ASP G 236 " pdb=" CA ASP G 236 " ideal model delta harmonic sigma weight residual 180.00 -143.98 -36.02 0 5.00e+00 4.00e-02 5.19e+01 ... (remaining 18912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4507 0.094 - 0.188: 354 0.188 - 0.282: 13 0.282 - 0.376: 1 0.376 - 0.469: 4 Chirality restraints: 4879 Sorted by residual: chirality pdb=" C19 1N7 L 701 " pdb=" C18 1N7 L 701 " pdb=" C2 1N7 L 701 " pdb=" C3 1N7 L 701 " both_signs ideal model delta sigma weight residual False -2.53 -3.00 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -2.99 0.46 2.00e-01 2.50e+01 5.20e+00 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 -2.98 0.45 2.00e-01 2.50e+01 5.08e+00 ... (remaining 4876 not shown) Planarity restraints: 5259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP I 485 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C ASP I 485 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP I 485 " 0.020 2.00e-02 2.50e+03 pdb=" N THR I 486 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 896 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO I 897 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO I 897 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 897 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J1325 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.87e+00 pdb=" C PHE J1325 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE J1325 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN J1326 " 0.017 2.00e-02 2.50e+03 ... (remaining 5256 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 634 2.64 - 3.21: 27603 3.21 - 3.77: 49457 3.77 - 4.34: 62852 4.34 - 4.90: 101388 Nonbonded interactions: 241934 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.077 2.170 nonbonded pdb=" OE1 GLU J 811 " pdb=" OG1 THR J 890 " model vdw 2.229 2.440 nonbonded pdb=" O THR J 528 " pdb=" OG1 THR J 528 " model vdw 2.247 2.440 nonbonded pdb=" O ASP L 514 " pdb=" OG SER L 517 " model vdw 2.251 2.440 nonbonded pdb=" N ASP H 15 " pdb=" OD1 ASP H 15 " model vdw 2.258 2.520 ... (remaining 241929 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 5 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 5 through 233) } 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: 0.700 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: 6.330 Check model and map are aligned: 0.480 Set scattering table: 0.250 Process input model: 90.390 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.292 31269 Z= 0.568 Angle : 0.864 18.306 42583 Z= 0.485 Chirality : 0.052 0.469 4879 Planarity : 0.006 0.076 5259 Dihedral : 17.323 172.190 12097 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.85 % Favored : 91.10 % Rotamer Outliers : 7.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.17 % 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: -2.11 (0.13), residues: 3651 helix: -0.21 (0.13), residues: 1377 sheet: -1.69 (0.24), residues: 435 loop : -2.30 (0.13), residues: 1839 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 148 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 233 outliers final: 110 residues processed: 370 average time/residue: 0.3689 time to fit residues: 232.5414 Evaluate side-chains 241 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 131 time to evaluate : 3.591 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 0 residues processed: 110 average time/residue: 0.2723 time to fit residues: 61.8947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 4.9990 chunk 281 optimal weight: 50.0000 chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 291 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 337 optimal weight: 50.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 HIS H 194 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1209 GLN J 153 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN J 365 GLN J 465 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 31269 Z= 0.157 Angle : 0.572 10.603 42583 Z= 0.299 Chirality : 0.041 0.167 4879 Planarity : 0.004 0.072 5259 Dihedral : 14.983 172.567 4835 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.06 % 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: -1.40 (0.13), residues: 3651 helix: 0.63 (0.14), residues: 1381 sheet: -1.52 (0.23), residues: 465 loop : -2.06 (0.13), residues: 1805 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 152 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 19 residues processed: 208 average time/residue: 0.3855 time to fit residues: 137.4442 Evaluate side-chains 154 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 3.569 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2797 time to fit residues: 14.9059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 281 optimal weight: 50.0000 chunk 230 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 338 optimal weight: 20.0000 chunk 365 optimal weight: 50.0000 chunk 301 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 271 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN I1209 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J1010 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 31269 Z= 0.464 Angle : 0.701 9.387 42583 Z= 0.361 Chirality : 0.044 0.153 4879 Planarity : 0.005 0.074 5259 Dihedral : 15.022 172.485 4835 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.29 % Favored : 90.61 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % 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: -1.28 (0.14), residues: 3651 helix: 0.81 (0.14), residues: 1387 sheet: -1.62 (0.23), residues: 473 loop : -2.03 (0.14), residues: 1791 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 134 time to evaluate : 3.863 Fit side-chains revert: symmetry clash outliers start: 114 outliers final: 54 residues processed: 238 average time/residue: 0.3817 time to fit residues: 156.7580 Evaluate side-chains 182 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 128 time to evaluate : 3.784 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.3100 time to fit residues: 36.1262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 9.9990 chunk 254 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 chunk 359 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 321 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I 955 GLN J 153 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 365 GLN J1010 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 31269 Z= 0.156 Angle : 0.544 8.584 42583 Z= 0.284 Chirality : 0.040 0.151 4879 Planarity : 0.004 0.069 5259 Dihedral : 14.804 171.132 4835 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3651 helix: 1.16 (0.14), residues: 1380 sheet: -1.30 (0.25), residues: 429 loop : -1.82 (0.14), residues: 1842 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 143 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 20 residues processed: 193 average time/residue: 0.3975 time to fit residues: 131.2127 Evaluate side-chains 158 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 3.509 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2428 time to fit residues: 13.1090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 322 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN I1288 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 31269 Z= 0.395 Angle : 0.638 8.895 42583 Z= 0.329 Chirality : 0.043 0.149 4879 Planarity : 0.004 0.068 5259 Dihedral : 14.838 171.407 4835 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.85 % Favored : 91.07 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3651 helix: 1.15 (0.14), residues: 1382 sheet: -1.44 (0.23), residues: 476 loop : -1.85 (0.14), residues: 1793 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 136 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 33 residues processed: 203 average time/residue: 0.4016 time to fit residues: 139.7043 Evaluate side-chains 166 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 3.659 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2825 time to fit residues: 22.6081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 5.9990 chunk 323 optimal weight: 0.0040 chunk 71 optimal weight: 40.0000 chunk 211 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 188 optimal weight: 0.1980 overall best weight: 2.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 31269 Z= 0.210 Angle : 0.554 9.847 42583 Z= 0.288 Chirality : 0.041 0.157 4879 Planarity : 0.004 0.068 5259 Dihedral : 14.765 171.068 4835 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.29 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3651 helix: 1.29 (0.14), residues: 1381 sheet: -1.31 (0.24), residues: 462 loop : -1.73 (0.14), residues: 1808 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 15 residues processed: 182 average time/residue: 0.4010 time to fit residues: 123.9975 Evaluate side-chains 153 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 3.672 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2811 time to fit residues: 12.9549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 262 optimal weight: 0.0170 chunk 203 optimal weight: 4.9990 chunk 302 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 31269 Z= 0.322 Angle : 0.606 10.400 42583 Z= 0.311 Chirality : 0.042 0.288 4879 Planarity : 0.004 0.068 5259 Dihedral : 14.768 171.114 4835 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.49 % Favored : 91.40 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3651 helix: 1.23 (0.14), residues: 1391 sheet: -1.38 (0.24), residues: 472 loop : -1.76 (0.14), residues: 1788 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 139 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 177 average time/residue: 0.4280 time to fit residues: 127.9764 Evaluate side-chains 154 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 3.748 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3402 time to fit residues: 16.2338 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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: 58.8245 > 50: distance: 5 - 28: 7.815 distance: 10 - 37: 11.023 distance: 15 - 48: 9.506 distance: 19 - 20: 3.861 distance: 20 - 21: 8.552 distance: 20 - 23: 8.125 distance: 21 - 22: 10.805 distance: 21 - 28: 7.292 distance: 23 - 24: 5.154 distance: 24 - 25: 3.428 distance: 25 - 26: 7.412 distance: 25 - 27: 14.144 distance: 28 - 29: 8.529 distance: 29 - 30: 8.588 distance: 29 - 32: 3.408 distance: 30 - 31: 6.124 distance: 30 - 37: 15.860 distance: 32 - 33: 6.747 distance: 33 - 34: 9.194 distance: 34 - 36: 9.544 distance: 37 - 38: 4.613 distance: 38 - 39: 4.192 distance: 38 - 41: 7.611 distance: 39 - 40: 7.725 distance: 39 - 48: 7.157 distance: 41 - 42: 5.801 distance: 42 - 44: 4.845 distance: 45 - 47: 4.218 distance: 46 - 47: 5.489 distance: 48 - 49: 6.477 distance: 49 - 50: 5.680 distance: 49 - 52: 9.092 distance: 50 - 51: 17.879 distance: 50 - 57: 19.514 distance: 52 - 53: 14.736 distance: 53 - 54: 13.201 distance: 54 - 55: 12.843 distance: 54 - 56: 11.727 distance: 57 - 58: 5.345 distance: 58 - 59: 13.157 distance: 58 - 61: 8.383 distance: 59 - 60: 15.889 distance: 59 - 63: 22.133 distance: 61 - 62: 13.130 distance: 63 - 64: 19.988 distance: 65 - 66: 11.908 distance: 65 - 67: 9.815 distance: 67 - 68: 20.833 distance: 68 - 69: 16.224 distance: 68 - 71: 24.099 distance: 69 - 70: 38.794 distance: 69 - 75: 14.787 distance: 71 - 72: 16.139 distance: 72 - 73: 11.254 distance: 72 - 74: 27.657 distance: 75 - 76: 12.670 distance: 76 - 77: 16.914 distance: 76 - 79: 17.236 distance: 77 - 78: 19.264 distance: 77 - 82: 3.940 distance: 79 - 80: 21.222 distance: 79 - 81: 16.502 distance: 82 - 83: 7.681 distance: 83 - 84: 11.754 distance: 83 - 86: 10.732 distance: 84 - 85: 4.299 distance: 84 - 89: 9.938 distance: 86 - 87: 3.116 distance: 86 - 88: 6.937 distance: 89 - 90: 7.396 distance: 90 - 91: 22.402 distance: 90 - 93: 6.548 distance: 91 - 92: 8.368 distance: 91 - 94: 9.137 distance: 92 - 115: 9.939