Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 10:37:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/10_2023/7xsq_33431.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/10_2023/7xsq_33431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/10_2023/7xsq_33431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/10_2023/7xsq_33431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/10_2023/7xsq_33431.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/10_2023/7xsq_33431.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.043 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 34 5.49 5 S 58 5.16 5 C 10416 2.51 5 N 2871 2.21 5 O 3190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A ASP 324": "OD1" <-> "OD2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ASP 520": "OD1" <-> "OD2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 542": "OD1" <-> "OD2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A ASP 686": "OD1" <-> "OD2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A ASP 793": "OD1" <-> "OD2" Residue "A ASP 801": "OD1" <-> "OD2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 833": "OD1" <-> "OD2" Residue "A ASP 869": "OD1" <-> "OD2" Residue "A ASP 870": "OD1" <-> "OD2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A TYR 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 914": "OD1" <-> "OD2" Residue "A TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 928": "OD1" <-> "OD2" Residue "A GLU 936": "OE1" <-> "OE2" Residue "A ASP 938": "OD1" <-> "OD2" Residue "A PHE 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A ASP 968": "OD1" <-> "OD2" Residue "A ASP 971": "OD1" <-> "OD2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A GLU 995": "OE1" <-> "OE2" Residue "A PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1411": "OD1" <-> "OD2" Residue "A PHE 1420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1460": "OE1" <-> "OE2" Residue "A ASP 1470": "OD1" <-> "OD2" Residue "A TYR 1481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1496": "OE1" <-> "OE2" Residue "A ASP 1513": "OD1" <-> "OD2" Residue "A GLU 1525": "OE1" <-> "OE2" Residue "A GLU 1529": "OE1" <-> "OE2" Residue "A ASP 1540": "OD1" <-> "OD2" Residue "A TYR 1555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1589": "OE1" <-> "OE2" Residue "A GLU 1640": "OE1" <-> "OE2" Residue "A ASP 1642": "OD1" <-> "OD2" Residue "A TYR 1663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1670": "OD1" <-> "OD2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B ASP 330": "OD1" <-> "OD2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B ASP 475": "OD1" <-> "OD2" Residue "B GLU 512": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B ASP 534": "OD1" <-> "OD2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B ASP 630": "OD1" <-> "OD2" Residue "B ASP 637": "OD1" <-> "OD2" Residue "B ASP 640": "OD1" <-> "OD2" Residue "B GLU 641": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "B GLU 678": "OE1" <-> "OE2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "B TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 690": "OE1" <-> "OE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 16573 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1289, 10360 Classifications: {'peptide': 1289} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1228} Chain breaks: 4 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 5497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5497 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 20, 'TRANS': 657} Chain breaks: 1 Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 4, 'rna3p_pyr': 12} Link IDs: {'rna2p': 18, 'rna3p': 15} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 676 SG CYS A 88 73.809 53.222 16.483 1.00 45.82 S ATOM 947 SG CYS A 121 76.522 51.899 14.048 1.00 61.32 S ATOM 993 SG CYS A 127 76.225 56.086 15.747 1.00 45.94 S ATOM 1017 SG CYS A 130 77.046 53.458 18.103 1.00 42.70 S ATOM 3719 SG CYS A 491 52.437 61.408 42.912 1.00 46.51 S ATOM 3787 SG CYS A 501 53.083 59.323 39.953 1.00 44.14 S ATOM 3801 SG CYS A 503 51.299 62.610 39.196 1.00 43.50 S ATOM 3823 SG CYS A 506 54.777 63.351 39.866 1.00 41.76 S ATOM 5794 SG CYS A 750 39.273 68.362 70.149 1.00 58.43 S ATOM 5807 SG CYS A 752 37.664 71.672 69.253 1.00 50.96 S ATOM 5829 SG CYS A 755 41.156 71.793 68.251 1.00 44.65 S ATOM 7828 SG CYS A1018 41.571 94.247 99.201 1.00 43.48 S ATOM 8053 SG CYS A1406 41.983 90.729 97.844 1.00 47.50 S ATOM 8104 SG CYS A1414 38.207 92.683 97.500 1.00 40.99 S ATOM 8121 SG CYS A1417 40.861 93.151 95.074 1.00 36.65 S Time building chain proxies: 8.76, per 1000 atoms: 0.53 Number of scatterers: 16573 At special positions: 0 Unit cell: (107.73, 149.625, 134.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 58 16.00 P 34 15.00 O 3190 8.00 N 2871 7.00 C 10416 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: 5.93 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 121 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " Number of angles added : 21 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3646 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 21 sheets defined 40.0% alpha, 16.4% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 5.75 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.748A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 267 through 287 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.493A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 removed outlier: 5.776A pdb=" N GLY A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 350 through 353 removed outlier: 3.918A pdb=" N ILE A 353 " --> pdb=" O ASN A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 354 through 375 removed outlier: 3.520A pdb=" N PHE A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.532A pdb=" N LEU A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 569 through 580 removed outlier: 3.741A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.630A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 631 through 636' Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.641A pdb=" N CYS A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 658 " --> pdb=" O ARG A 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 658' Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 723 through 739 removed outlier: 3.669A pdb=" N HIS A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 758 Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 873 through 882 Processing helix chain 'A' and resid 909 through 914 removed outlier: 4.330A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.801A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 removed outlier: 3.884A pdb=" N LEU A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1404 Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1463 through 1467 removed outlier: 3.628A pdb=" N PHE A1466 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.756A pdb=" N LYS A1493 " --> pdb=" O ILE A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1499 removed outlier: 3.613A pdb=" N ILE A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A1499 " --> pdb=" O LEU A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 Processing helix chain 'A' and resid 1583 through 1603 removed outlier: 3.519A pdb=" N ILE A1587 " --> pdb=" O PRO A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.614A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1673 through 1683 removed outlier: 3.513A pdb=" N ARG A1677 " --> pdb=" O PRO A1673 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 32 Processing helix chain 'B' and resid 37 through 59 removed outlier: 4.231A pdb=" N LYS B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.842A pdb=" N PHE B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.870A pdb=" N LYS B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 136 Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.583A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 190 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 208 through 224 removed outlier: 3.640A pdb=" N ALA B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 246 removed outlier: 4.354A pdb=" N ASP B 234 " --> pdb=" O HIS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.810A pdb=" N ILE B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 297 removed outlier: 3.547A pdb=" N LEU B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 322 Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 340 through 362 removed outlier: 4.081A pdb=" N TYR B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 451 removed outlier: 3.587A pdb=" N PHE B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 Processing helix chain 'B' and resid 470 through 474 removed outlier: 3.807A pdb=" N PHE B 473 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 509 through 513 removed outlier: 3.611A pdb=" N GLU B 512 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 513 " --> pdb=" O PHE B 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 509 through 513' Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 547 through 552 Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.566A pdb=" N LEU B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 596 removed outlier: 3.808A pdb=" N SER B 596 " --> pdb=" O PRO B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.936A pdb=" N ALA B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.868A pdb=" N THR B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 691 removed outlier: 3.972A pdb=" N TRP B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.554A pdb=" N PHE B 703 " --> pdb=" O HIS B 699 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.857A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 18 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP A 195 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 13.759A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 4.113A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 9 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.302A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 7.154A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.601A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.601A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.866A pdb=" N VAL A 432 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB2, first strand: chain 'A' and resid 533 through 534 removed outlier: 3.838A pdb=" N THR A 539 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.979A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.979A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB6, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.884A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.884A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS A 957 " --> pdb=" O ILE A1564 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE A1564 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU A 959 " --> pdb=" O ILE A1562 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A1562 " --> pdb=" O GLU A 959 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 985 through 986 removed outlier: 6.679A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 425 through 431 Processing sheet with id=AC2, first strand: chain 'B' and resid 536 through 540 removed outlier: 5.193A pdb=" N THR B 660 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA B 626 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 585 through 587 removed outlier: 4.390A pdb=" N HIS B 585 " --> pdb=" O LYS B 599 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1854 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 8.33 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 2709 1.26 - 1.40: 4287 1.40 - 1.54: 9626 1.54 - 1.67: 308 1.67 - 1.81: 81 Bond restraints: 17011 Sorted by residual: bond pdb=" C PRO A1687 " pdb=" O PRO A1687 " ideal model delta sigma weight residual 1.233 1.125 0.108 1.19e-02 7.06e+03 8.21e+01 bond pdb=" C TRP A1688 " pdb=" O TRP A1688 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.33e-02 5.65e+03 1.73e+01 bond pdb=" C TYR A 921 " pdb=" N TYR A 922 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.07e-02 2.33e+03 1.10e+01 bond pdb=" N PRO A1690 " pdb=" CD PRO A1690 " ideal model delta sigma weight residual 1.474 1.430 0.044 1.40e-02 5.10e+03 9.94e+00 bond pdb=" N PHE A1691 " pdb=" CA PHE A1691 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.34e-02 5.57e+03 6.43e+00 ... (remaining 17006 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.58: 348 104.58 - 112.10: 8085 112.10 - 119.61: 6298 119.61 - 127.13: 8091 127.13 - 134.64: 275 Bond angle restraints: 23097 Sorted by residual: angle pdb=" C PRO A1687 " pdb=" CA PRO A1687 " pdb=" CB PRO A1687 " ideal model delta sigma weight residual 111.23 102.89 8.34 1.28e+00 6.10e-01 4.24e+01 angle pdb=" N PRO A1690 " pdb=" CD PRO A1690 " pdb=" CG PRO A1690 " ideal model delta sigma weight residual 103.80 97.07 6.73 1.20e+00 6.94e-01 3.15e+01 angle pdb=" N PRO A1687 " pdb=" CA PRO A1687 " pdb=" C PRO A1687 " ideal model delta sigma weight residual 111.21 118.89 -7.68 1.59e+00 3.96e-01 2.33e+01 angle pdb=" C SER A 396 " pdb=" N GLU A 397 " pdb=" CA GLU A 397 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" CA ASN A1649 " pdb=" CB ASN A1649 " pdb=" CG ASN A1649 " ideal model delta sigma weight residual 112.60 117.07 -4.47 1.00e+00 1.00e+00 2.00e+01 ... (remaining 23092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.95: 9823 34.95 - 69.91: 314 69.91 - 104.86: 16 104.86 - 139.82: 1 139.82 - 174.77: 9 Dihedral angle restraints: 10163 sinusoidal: 4491 harmonic: 5672 Sorted by residual: dihedral pdb=" CA GLU A1650 " pdb=" C GLU A1650 " pdb=" N GLU A1651 " pdb=" CA GLU A1651 " ideal model delta harmonic sigma weight residual 180.00 -124.45 -55.55 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 34.55 165.45 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' U D 8 " pdb=" C1' U D 8 " pdb=" N1 U D 8 " pdb=" C2 U D 8 " ideal model delta sinusoidal sigma weight residual 200.00 39.73 160.27 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 10160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1859 0.059 - 0.118: 500 0.118 - 0.177: 111 0.177 - 0.236: 15 0.236 - 0.294: 8 Chirality restraints: 2493 Sorted by residual: chirality pdb=" CA ASN A1649 " pdb=" N ASN A1649 " pdb=" C ASN A1649 " pdb=" CB ASN A1649 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB VAL A 377 " pdb=" CA VAL A 377 " pdb=" CG1 VAL A 377 " pdb=" CG2 VAL A 377 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1' C D 13 " pdb=" O4' C D 13 " pdb=" C2' C D 13 " pdb=" N1 C D 13 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2490 not shown) Planarity restraints: 2854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 962 " -0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO A 963 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 963 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 963 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 297 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ALA A 297 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA A 297 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 298 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 700 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.95e+00 pdb=" N PRO B 701 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 701 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 701 " 0.045 5.00e-02 4.00e+02 ... (remaining 2851 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 574 2.71 - 3.25: 14512 3.25 - 3.80: 24888 3.80 - 4.35: 31649 4.35 - 4.90: 54924 Nonbonded interactions: 126547 Sorted by model distance: nonbonded pdb=" O SER A 449 " pdb=" OG SER A 449 " model vdw 2.157 2.440 nonbonded pdb=" O THR B 87 " pdb=" OG1 THR B 87 " model vdw 2.266 2.440 nonbonded pdb=" O ASN A 179 " pdb=" O2' G D -3 " model vdw 2.268 2.440 nonbonded pdb=" O THR A 969 " pdb=" OG1 THR A 969 " model vdw 2.269 2.440 nonbonded pdb=" O PHE A 104 " pdb=" O2' G D -9 " model vdw 2.318 2.440 ... (remaining 126542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 5.440 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 51.690 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 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 0.108 17011 Z= 0.562 Angle : 0.931 9.797 23097 Z= 0.520 Chirality : 0.059 0.294 2493 Planarity : 0.008 0.089 2854 Dihedral : 17.105 174.774 6517 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 2.74 % Allowed : 11.42 % Favored : 85.85 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 0.11 % 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: -2.88 (0.15), residues: 1953 helix: -1.78 (0.15), residues: 686 sheet: -0.49 (0.31), residues: 248 loop : -2.41 (0.15), residues: 1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 414 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 12 residues processed: 449 average time/residue: 1.3533 time to fit residues: 673.9623 Evaluate side-chains 344 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 332 time to evaluate : 1.812 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 5 average time/residue: 0.2003 time to fit residues: 4.3510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 287 ASN A 306 HIS A 664 ASN A 871 ASN A 881 ASN A 993 ASN A1506 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 ASN A1604 ASN B 109 ASN B 112 ASN B 142 ASN B 194 ASN B 210 HIS B 446 ASN B 513 ASN B 514 HIS B 572 ASN B 576 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17011 Z= 0.262 Angle : 0.652 8.389 23097 Z= 0.342 Chirality : 0.045 0.282 2493 Planarity : 0.006 0.061 2854 Dihedral : 13.373 177.736 2535 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 3.96 % Allowed : 19.98 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 1953 helix: 0.09 (0.18), residues: 702 sheet: -0.36 (0.30), residues: 267 loop : -1.99 (0.16), residues: 984 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 397 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 26 residues processed: 428 average time/residue: 1.4042 time to fit residues: 664.4272 Evaluate side-chains 382 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 356 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 17 residues processed: 10 average time/residue: 0.4324 time to fit residues: 8.1740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 61 optimal weight: 0.0970 chunk 144 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 119 ASN A 138 ASN A 306 HIS A 534 ASN A1506 ASN A1649 ASN B 210 HIS B 448 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17011 Z= 0.397 Angle : 0.710 9.378 23097 Z= 0.369 Chirality : 0.049 0.293 2493 Planarity : 0.006 0.060 2854 Dihedral : 13.499 177.880 2535 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 4.66 % Allowed : 22.89 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 1953 helix: 0.83 (0.20), residues: 700 sheet: -0.21 (0.30), residues: 266 loop : -1.85 (0.17), residues: 987 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 401 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 41 residues processed: 443 average time/residue: 1.4160 time to fit residues: 695.7891 Evaluate side-chains 411 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 370 time to evaluate : 1.747 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 28 residues processed: 15 average time/residue: 0.8790 time to fit residues: 18.0189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 120 optimal weight: 0.1980 chunk 180 optimal weight: 0.4980 chunk 191 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN A 459 ASN A 955 ASN A1506 ASN A1592 ASN A1596 GLN ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17011 Z= 0.166 Angle : 0.569 10.011 23097 Z= 0.296 Chirality : 0.042 0.259 2493 Planarity : 0.005 0.054 2854 Dihedral : 13.239 178.804 2535 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 4.19 % Allowed : 24.87 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.18), residues: 1953 helix: 1.44 (0.20), residues: 693 sheet: -0.00 (0.30), residues: 275 loop : -1.65 (0.18), residues: 985 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 354 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 38 residues processed: 398 average time/residue: 1.4047 time to fit residues: 618.6670 Evaluate side-chains 378 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 340 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 14 average time/residue: 0.3155 time to fit residues: 8.8256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 142 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 97 optimal weight: 0.0670 chunk 171 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN A1506 ASN B 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17011 Z= 0.164 Angle : 0.541 10.478 23097 Z= 0.281 Chirality : 0.042 0.271 2493 Planarity : 0.004 0.058 2854 Dihedral : 13.102 179.323 2535 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 4.08 % Allowed : 25.33 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1953 helix: 1.78 (0.20), residues: 693 sheet: 0.11 (0.31), residues: 271 loop : -1.44 (0.18), residues: 989 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 353 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 35 residues processed: 393 average time/residue: 1.4035 time to fit residues: 610.3347 Evaluate side-chains 378 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 343 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 24 residues processed: 13 average time/residue: 0.6890 time to fit residues: 13.2844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 15 optimal weight: 0.0000 chunk 63 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN A1568 HIS A1592 ASN A1596 GLN B 210 HIS B 513 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17011 Z= 0.166 Angle : 0.538 9.033 23097 Z= 0.280 Chirality : 0.041 0.240 2493 Planarity : 0.004 0.058 2854 Dihedral : 13.064 179.473 2535 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 3.61 % Allowed : 26.67 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1953 helix: 2.00 (0.20), residues: 691 sheet: 0.22 (0.31), residues: 275 loop : -1.36 (0.18), residues: 987 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 352 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 37 residues processed: 389 average time/residue: 1.3819 time to fit residues: 595.6879 Evaluate side-chains 386 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 349 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 24 residues processed: 13 average time/residue: 0.8080 time to fit residues: 14.9330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 119 optimal weight: 0.0570 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS A 993 ASN A1506 ASN A1596 GLN B 210 HIS B 513 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17011 Z= 0.260 Angle : 0.598 9.542 23097 Z= 0.310 Chirality : 0.044 0.249 2493 Planarity : 0.005 0.063 2854 Dihedral : 13.182 178.425 2535 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 3.79 % Allowed : 26.44 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1953 helix: 1.97 (0.20), residues: 690 sheet: 0.30 (0.31), residues: 270 loop : -1.44 (0.18), residues: 993 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 370 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 42 residues processed: 404 average time/residue: 1.3838 time to fit residues: 620.0297 Evaluate side-chains 399 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 357 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 27 residues processed: 17 average time/residue: 0.5030 time to fit residues: 13.5982 ------------------------------------------------------------------------------- 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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 65.6525 > 50: distance: 16 - 20: 27.575 distance: 20 - 21: 28.859 distance: 21 - 22: 33.007 distance: 21 - 24: 28.793 distance: 22 - 23: 30.916 distance: 22 - 28: 19.597 distance: 24 - 25: 43.719 distance: 25 - 26: 65.652 distance: 25 - 27: 54.861 distance: 28 - 29: 25.602 distance: 28 - 34: 26.992 distance: 29 - 30: 21.351 distance: 29 - 32: 23.264 distance: 30 - 31: 20.011 distance: 30 - 35: 38.677 distance: 32 - 33: 38.843 distance: 33 - 34: 53.387 distance: 35 - 36: 47.168 distance: 36 - 37: 8.825 distance: 36 - 39: 30.285 distance: 37 - 38: 51.016 distance: 37 - 46: 51.163 distance: 39 - 40: 59.007 distance: 40 - 41: 40.683 distance: 41 - 42: 32.408 distance: 42 - 43: 17.716 distance: 43 - 44: 4.091 distance: 43 - 45: 12.229 distance: 46 - 47: 21.973 distance: 47 - 48: 38.480 distance: 47 - 50: 30.664 distance: 48 - 49: 40.231 distance: 48 - 53: 22.690 distance: 50 - 51: 45.554 distance: 50 - 52: 41.567 distance: 53 - 54: 34.322 distance: 54 - 55: 17.447 distance: 54 - 57: 10.565 distance: 55 - 56: 17.745 distance: 55 - 62: 28.676 distance: 56 - 84: 20.174 distance: 57 - 58: 18.913 distance: 58 - 59: 14.678 distance: 59 - 60: 9.037 distance: 62 - 63: 29.302 distance: 62 - 68: 24.361 distance: 63 - 64: 30.028 distance: 63 - 66: 42.727 distance: 64 - 65: 33.393 distance: 64 - 69: 41.607 distance: 65 - 95: 43.982 distance: 66 - 67: 50.246 distance: 67 - 68: 19.633 distance: 69 - 70: 25.116 distance: 70 - 71: 23.780 distance: 70 - 73: 30.872 distance: 71 - 72: 17.018 distance: 71 - 76: 11.136 distance: 73 - 74: 23.712 distance: 73 - 75: 15.582 distance: 76 - 77: 9.011 distance: 77 - 78: 21.195 distance: 77 - 80: 21.741 distance: 78 - 79: 18.621 distance: 78 - 84: 8.785 distance: 79 - 113: 13.055 distance: 80 - 81: 27.749 distance: 81 - 82: 24.874 distance: 81 - 83: 29.723 distance: 84 - 85: 15.120 distance: 85 - 86: 18.019 distance: 85 - 88: 36.603 distance: 86 - 87: 29.724 distance: 86 - 95: 18.472 distance: 87 - 120: 11.845 distance: 88 - 89: 28.250 distance: 89 - 90: 14.796 distance: 90 - 91: 4.595 distance: 91 - 92: 4.092 distance: 92 - 93: 3.271 distance: 92 - 94: 3.770 distance: 95 - 96: 31.056 distance: 96 - 97: 13.646 distance: 96 - 99: 5.352 distance: 97 - 98: 40.118 distance: 97 - 104: 21.258 distance: 99 - 100: 39.752 distance: 100 - 101: 14.099 distance: 101 - 102: 11.768 distance: 102 - 103: 7.939