Starting phenix.real_space_refine (version: dev) on Wed Mar 15 21:39:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2023/7n4u_24178_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2023/7n4u_24178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2023/7n4u_24178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2023/7n4u_24178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2023/7n4u_24178_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2023/7n4u_24178_updated.pdb" } resolution = 3.34 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= 0.005 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 Process input model Symmetric amino acids flipped Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 956": "OD1" <-> "OD2" Residue "A ASP 959": "OD1" <-> "OD2" Residue "A ASP 1018": "OD1" <-> "OD2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1199": "OE1" <-> "OE2" Residue "A ASP 1268": "OD1" <-> "OD2" Residue "A GLU 1276": "OE1" <-> "OE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ASP 469": "OD1" <-> "OD2" Residue "B PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 742": "NH1" <-> "NH2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "B GLU 825": "OE1" <-> "OE2" Residue "B ASP 872": "OD1" <-> "OD2" Residue "B GLU 874": "OE1" <-> "OE2" Residue "B TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 956": "OD1" <-> "OD2" Residue "B ASP 959": "OD1" <-> "OD2" Residue "B ASP 1018": "OD1" <-> "OD2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B ARG 1136": "NH1" <-> "NH2" Residue "B PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1199": "OE1" <-> "OE2" Residue "B ASP 1268": "OD1" <-> "OD2" Residue "B GLU 1276": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 15396 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7426 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "B" Number of atoms: 7426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7426 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 188 Unusual residues: {'CLR': 2, 'NAG': 4, 'POV': 1, 'VIV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 188 Unusual residues: {'CLR': 2, 'NAG': 4, 'POV': 1, 'VIV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.69, per 1000 atoms: 0.56 Number of scatterers: 15396 At special positions: 0 Unit cell: (134.113, 89.131, 136.612, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 2 15.00 O 2802 8.00 N 2434 7.00 C 10068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1024 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B 966 " - pdb=" SG CYS B1024 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B 993 " distance=2.03 Simple disulfide: pdb=" SG CYS B 980 " - pdb=" SG CYS B 989 " distance=2.03 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 Atom "HETATM15032 O5 NAG A1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM15265 O5 NAG B1602 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1401 " - " ASN A 431 " " NAG A1402 " - " ASN A 464 " " NAG A1403 " - " ASN A1075 " " NAG A1404 " - " ASN A 506 " " NAG B1602 " - " ASN B 431 " " NAG B1603 " - " ASN B 464 " " NAG B1604 " - " ASN B1075 " " NAG B1605 " - " ASN B 506 " " NAG C 1 " - " ASN A 497 " " NAG D 1 " - " ASN A 909 " " NAG E 1 " - " ASN A1037 " " NAG F 1 " - " ASN B 497 " " NAG G 1 " - " ASN B 909 " " NAG H 1 " - " ASN B1037 " Time building additional restraints: 6.17 Conformation dependent library (CDL) restraints added in 2.1 seconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 10 sheets defined 56.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 334 through 350 removed outlier: 3.615A pdb=" N SER A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 372 Proline residue: A 362 - end of helix removed outlier: 4.734A pdb=" N GLY A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 518 through 527 removed outlier: 3.728A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 555 No H-bonds generated for 'chain 'A' and resid 552 through 555' Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 584 through 606 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 628 through 631 No H-bonds generated for 'chain 'A' and resid 628 through 631' Processing helix chain 'A' and resid 633 through 651 removed outlier: 3.919A pdb=" N THR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 666 through 689 Processing helix chain 'A' and resid 696 through 709 Proline residue: A 703 - end of helix removed outlier: 3.612A pdb=" N LEU A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 Processing helix chain 'A' and resid 732 through 763 Proline residue: A 745 - end of helix removed outlier: 4.510A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 803 removed outlier: 3.751A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 840 removed outlier: 5.418A pdb=" N ALA A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 843 through 865 removed outlier: 4.419A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.119A pdb=" N ILE A 919 " --> pdb=" O GLY A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.783A pdb=" N GLU A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 960 Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 1005 through 1016 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1028 through 1031 No H-bonds generated for 'chain 'A' and resid 1028 through 1031' Processing helix chain 'A' and resid 1059 through 1080 removed outlier: 3.552A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1106 No H-bonds generated for 'chain 'A' and resid 1104 through 1106' Processing helix chain 'A' and resid 1108 through 1130 Proline residue: A1122 - end of helix removed outlier: 3.720A pdb=" N LEU A1129 " --> pdb=" O ALA A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1159 Processing helix chain 'A' and resid 1165 through 1190 removed outlier: 4.450A pdb=" N VAL A1179 " --> pdb=" O VAL A1175 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLU A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1225 removed outlier: 3.967A pdb=" N SER A1210 " --> pdb=" O ILE A1206 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA A1211 " --> pdb=" O SER A1207 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1227 through 1229 No H-bonds generated for 'chain 'A' and resid 1227 through 1229' Processing helix chain 'A' and resid 1233 through 1238 Processing helix chain 'A' and resid 1240 through 1265 removed outlier: 5.318A pdb=" N LEU A1258 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1271 through 1273 No H-bonds generated for 'chain 'A' and resid 1271 through 1273' Processing helix chain 'B' and resid 334 through 350 removed outlier: 3.619A pdb=" N SER B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 372 Proline residue: B 362 - end of helix removed outlier: 4.734A pdb=" N GLY B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 382 No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 389 through 401 Processing helix chain 'B' and resid 434 through 436 No H-bonds generated for 'chain 'B' and resid 434 through 436' Processing helix chain 'B' and resid 438 through 452 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 498 through 501 No H-bonds generated for 'chain 'B' and resid 498 through 501' Processing helix chain 'B' and resid 518 through 527 removed outlier: 3.726A pdb=" N ASN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 555 No H-bonds generated for 'chain 'B' and resid 552 through 555' Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 584 through 606 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 628 through 631 No H-bonds generated for 'chain 'B' and resid 628 through 631' Processing helix chain 'B' and resid 633 through 651 removed outlier: 3.919A pdb=" N THR B 638 " --> pdb=" O PRO B 634 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 663 No H-bonds generated for 'chain 'B' and resid 660 through 663' Processing helix chain 'B' and resid 666 through 689 Processing helix chain 'B' and resid 696 through 709 Proline residue: B 703 - end of helix removed outlier: 3.611A pdb=" N LEU B 707 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 723 Processing helix chain 'B' and resid 732 through 763 Proline residue: B 745 - end of helix removed outlier: 4.513A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 803 removed outlier: 3.749A pdb=" N SER B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 792 " --> pdb=" O MET B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 840 removed outlier: 5.421A pdb=" N ALA B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) Proline residue: B 838 - end of helix Processing helix chain 'B' and resid 843 through 865 removed outlier: 4.420A pdb=" N GLY B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 876 No H-bonds generated for 'chain 'B' and resid 874 through 876' Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.120A pdb=" N ILE B 919 " --> pdb=" O GLY B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 939 removed outlier: 3.785A pdb=" N GLU B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 960 Processing helix chain 'B' and resid 987 through 989 No H-bonds generated for 'chain 'B' and resid 987 through 989' Processing helix chain 'B' and resid 1005 through 1016 Proline residue: B1013 - end of helix Processing helix chain 'B' and resid 1028 through 1031 No H-bonds generated for 'chain 'B' and resid 1028 through 1031' Processing helix chain 'B' and resid 1059 through 1080 removed outlier: 3.553A pdb=" N ASP B1079 " --> pdb=" O ASN B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1106 No H-bonds generated for 'chain 'B' and resid 1104 through 1106' Processing helix chain 'B' and resid 1108 through 1130 Proline residue: B1122 - end of helix removed outlier: 3.718A pdb=" N LEU B1129 " --> pdb=" O ALA B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1159 Processing helix chain 'B' and resid 1165 through 1190 removed outlier: 4.448A pdb=" N VAL B1179 " --> pdb=" O VAL B1175 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE B1181 " --> pdb=" O MET B1177 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS B1184 " --> pdb=" O GLU B1180 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE B1185 " --> pdb=" O PHE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1225 removed outlier: 3.968A pdb=" N SER B1210 " --> pdb=" O ILE B1206 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B1211 " --> pdb=" O SER B1207 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET B1218 " --> pdb=" O ALA B1214 " (cutoff:3.500A) Proline residue: B1222 - end of helix Processing helix chain 'B' and resid 1227 through 1229 No H-bonds generated for 'chain 'B' and resid 1227 through 1229' Processing helix chain 'B' and resid 1233 through 1238 Processing helix chain 'B' and resid 1240 through 1265 removed outlier: 5.323A pdb=" N LEU B1258 " --> pdb=" O GLY B1254 " (cutoff:3.500A) Proline residue: B1259 - end of helix Processing helix chain 'B' and resid 1271 through 1273 No H-bonds generated for 'chain 'B' and resid 1271 through 1273' Processing sheet with id= A, first strand: chain 'A' and resid 409 through 411 Processing sheet with id= B, first strand: chain 'A' and resid 419 through 423 Processing sheet with id= C, first strand: chain 'A' and resid 505 through 509 Processing sheet with id= D, first strand: chain 'A' and resid 1050 through 1052 Processing sheet with id= E, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.762A pdb=" N THR A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 409 through 411 Processing sheet with id= G, first strand: chain 'B' and resid 419 through 423 Processing sheet with id= H, first strand: chain 'B' and resid 505 through 509 Processing sheet with id= I, first strand: chain 'B' and resid 1050 through 1052 Processing sheet with id= J, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.762A pdb=" N THR B1046 " --> pdb=" O ASN B1037 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 6.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2384 1.31 - 1.44: 4270 1.44 - 1.57: 8980 1.57 - 1.69: 4 1.69 - 1.82: 138 Bond restraints: 15776 Sorted by residual: bond pdb=" C4 VIV B1608 " pdb=" O1 VIV B1608 " ideal model delta sigma weight residual 1.358 1.463 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C4 VIV A1407 " pdb=" O1 VIV A1407 " ideal model delta sigma weight residual 1.358 1.463 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" N VAL A 662 " pdb=" CA VAL A 662 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.09e+01 bond pdb=" N VAL B 662 " pdb=" CA VAL B 662 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.07e+01 bond pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.69e+01 ... (remaining 15771 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.98: 547 106.98 - 113.86: 8741 113.86 - 120.75: 6900 120.75 - 127.63: 5222 127.63 - 134.51: 90 Bond angle restraints: 21500 Sorted by residual: angle pdb=" C GLY B 671 " pdb=" N GLY B 672 " pdb=" CA GLY B 672 " ideal model delta sigma weight residual 119.94 125.32 -5.38 1.11e+00 8.12e-01 2.35e+01 angle pdb=" C GLY A 671 " pdb=" N GLY A 672 " pdb=" CA GLY A 672 " ideal model delta sigma weight residual 119.94 125.30 -5.36 1.11e+00 8.12e-01 2.33e+01 angle pdb=" C GLN A 342 " pdb=" N GLY A 343 " pdb=" CA GLY A 343 " ideal model delta sigma weight residual 119.94 125.09 -5.15 1.11e+00 8.12e-01 2.16e+01 angle pdb=" C GLN B 342 " pdb=" N GLY B 343 " pdb=" CA GLY B 343 " ideal model delta sigma weight residual 119.94 125.08 -5.14 1.11e+00 8.12e-01 2.15e+01 angle pdb=" C ALA A 914 " pdb=" N GLY A 915 " pdb=" CA GLY A 915 " ideal model delta sigma weight residual 119.94 125.04 -5.10 1.11e+00 8.12e-01 2.11e+01 ... (remaining 21495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.97: 8844 31.97 - 63.95: 290 63.95 - 95.92: 22 95.92 - 127.89: 0 127.89 - 159.87: 2 Dihedral angle restraints: 9158 sinusoidal: 3606 harmonic: 5552 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 159.81 -66.81 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" SG CYS B 542 " pdb=" CB CYS B 542 " ideal model delta sinusoidal sigma weight residual 93.00 159.76 -66.76 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS B 966 " pdb=" SG CYS B 966 " pdb=" SG CYS B1024 " pdb=" CB CYS B1024 " ideal model delta sinusoidal sigma weight residual 93.00 143.82 -50.82 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 9155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 2526 0.948 - 1.896: 2 1.896 - 2.844: 2 2.844 - 3.792: 2 3.792 - 4.740: 8 Chirality restraints: 2540 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.48e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.48e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 2.27 -4.67 2.00e-02 2.50e+03 5.45e+04 ... (remaining 2537 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG D 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.147 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG G 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1602 " 0.218 2.00e-02 2.50e+03 1.86e-01 4.31e+02 pdb=" C7 NAG B1602 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B1602 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG B1602 " -0.304 2.00e-02 2.50e+03 pdb=" O7 NAG B1602 " 0.169 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 190 2.66 - 3.22: 13908 3.22 - 3.78: 23980 3.78 - 4.34: 30549 4.34 - 4.90: 53896 Nonbonded interactions: 122523 Sorted by model distance: nonbonded pdb=" O VAL B 660 " pdb=" OD2 ASP B 808 " model vdw 2.102 3.040 nonbonded pdb=" O VAL A 660 " pdb=" OD2 ASP A 808 " model vdw 2.103 3.040 nonbonded pdb=" O VAL B 380 " pdb=" OG SER B 384 " model vdw 2.273 2.440 nonbonded pdb=" O VAL A 380 " pdb=" OG SER A 384 " model vdw 2.274 2.440 nonbonded pdb=" O MET A 661 " pdb=" N ASP A 808 " model vdw 2.360 2.520 ... (remaining 122518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 333 through 1285 or resid 1402 through 1404 or resid 1406) \ ) selection = (chain 'B' and (resid 333 through 1285 or resid 1602 through 1604 or resid 1606) \ ) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 90 5.16 5 C 10068 2.51 5 N 2434 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 10.640 Check model and map are aligned: 0.210 Process input model: 38.870 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.014 0.105 15776 Z= 0.920 Angle : 1.795 11.810 21500 Z= 1.328 Chirality : 0.294 4.740 2540 Planarity : 0.011 0.303 2650 Dihedral : 15.322 159.868 5542 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.53 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.17), residues: 1902 helix: -1.48 (0.13), residues: 1062 sheet: -2.56 (0.40), residues: 126 loop : -1.97 (0.22), residues: 714 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 206 average time/residue: 0.2581 time to fit residues: 81.7486 Evaluate side-chains 125 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.781 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1389 time to fit residues: 5.3194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 527 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1184 HIS A1253 HIS B 339 GLN B 409 GLN B 527 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1184 HIS B1220 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 15776 Z= 0.177 Angle : 0.690 11.629 21500 Z= 0.312 Chirality : 0.055 1.064 2540 Planarity : 0.003 0.043 2650 Dihedral : 9.265 135.527 2164 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.94 % Favored : 96.95 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1902 helix: 0.73 (0.16), residues: 1058 sheet: -2.07 (0.42), residues: 126 loop : -1.35 (0.23), residues: 718 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.783 Fit side-chains outliers start: 32 outliers final: 13 residues processed: 164 average time/residue: 0.2305 time to fit residues: 61.3754 Evaluate side-chains 119 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1540 time to fit residues: 5.9342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 172 optimal weight: 0.4980 chunk 186 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 171 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 138 optimal weight: 0.0060 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1220 ASN B1233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 15776 Z= 0.195 Angle : 0.614 11.059 21500 Z= 0.283 Chirality : 0.046 0.746 2540 Planarity : 0.003 0.032 2650 Dihedral : 8.503 118.208 2164 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.36 % Favored : 96.53 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1902 helix: 1.14 (0.16), residues: 1058 sheet: -1.86 (0.48), residues: 102 loop : -1.16 (0.23), residues: 742 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.995 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 142 average time/residue: 0.2490 time to fit residues: 58.9679 Evaluate side-chains 117 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 3.146 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1505 time to fit residues: 6.8665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 chunk 19 optimal weight: 0.0370 chunk 82 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 164 optimal weight: 6.9990 chunk 49 optimal weight: 0.0010 overall best weight: 0.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15776 Z= 0.129 Angle : 0.568 11.079 21500 Z= 0.262 Chirality : 0.042 0.618 2540 Planarity : 0.003 0.029 2650 Dihedral : 8.100 109.241 2164 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.00 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1902 helix: 1.36 (0.16), residues: 1060 sheet: -1.51 (0.50), residues: 102 loop : -0.95 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 134 average time/residue: 0.2407 time to fit residues: 52.8374 Evaluate side-chains 112 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 1.741 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1810 time to fit residues: 5.1436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 15776 Z= 0.222 Angle : 0.588 10.851 21500 Z= 0.272 Chirality : 0.043 0.554 2540 Planarity : 0.003 0.026 2650 Dihedral : 8.003 105.024 2164 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.37 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1902 helix: 1.27 (0.16), residues: 1068 sheet: -1.50 (0.50), residues: 102 loop : -0.83 (0.24), residues: 732 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.939 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 125 average time/residue: 0.2541 time to fit residues: 51.0547 Evaluate side-chains 108 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1527 time to fit residues: 5.1163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15776 Z= 0.189 Angle : 0.555 10.971 21500 Z= 0.257 Chirality : 0.041 0.520 2540 Planarity : 0.003 0.027 2650 Dihedral : 7.888 105.514 2164 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1902 helix: 1.33 (0.16), residues: 1056 sheet: -1.69 (0.50), residues: 106 loop : -0.89 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.901 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 119 average time/residue: 0.2711 time to fit residues: 50.4157 Evaluate side-chains 112 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1499 time to fit residues: 7.0799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 134 optimal weight: 0.2980 chunk 154 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 183 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 15776 Z= 0.144 Angle : 0.539 10.878 21500 Z= 0.250 Chirality : 0.040 0.486 2540 Planarity : 0.003 0.026 2650 Dihedral : 7.724 105.817 2164 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1902 helix: 1.49 (0.17), residues: 1052 sheet: -1.59 (0.48), residues: 118 loop : -0.77 (0.24), residues: 732 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.821 Fit side-chains outliers start: 17 outliers final: 5 residues processed: 116 average time/residue: 0.2598 time to fit residues: 48.2314 Evaluate side-chains 107 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2983 time to fit residues: 4.6591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 17 optimal weight: 0.0270 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15776 Z= 0.179 Angle : 0.549 10.635 21500 Z= 0.256 Chirality : 0.040 0.467 2540 Planarity : 0.003 0.026 2650 Dihedral : 7.681 104.531 2164 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1902 helix: 1.49 (0.16), residues: 1054 sheet: -1.54 (0.50), residues: 106 loop : -0.73 (0.24), residues: 742 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.897 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 110 average time/residue: 0.2777 time to fit residues: 48.8912 Evaluate side-chains 104 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1459 time to fit residues: 4.1581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 112 optimal weight: 0.0970 chunk 180 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 15776 Z= 0.158 Angle : 0.542 10.660 21500 Z= 0.252 Chirality : 0.040 0.458 2540 Planarity : 0.003 0.026 2650 Dihedral : 7.578 104.913 2164 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1902 helix: 1.54 (0.17), residues: 1056 sheet: -1.45 (0.50), residues: 106 loop : -0.67 (0.24), residues: 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.936 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 111 average time/residue: 0.2614 time to fit residues: 46.2069 Evaluate side-chains 108 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1854 time to fit residues: 4.2731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 0.0980 chunk 119 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15776 Z= 0.202 Angle : 0.563 10.621 21500 Z= 0.263 Chirality : 0.040 0.448 2540 Planarity : 0.003 0.026 2650 Dihedral : 7.582 104.103 2164 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1902 helix: 1.53 (0.17), residues: 1054 sheet: -1.48 (0.50), residues: 106 loop : -0.66 (0.24), residues: 742 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.940 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 98 average time/residue: 0.2736 time to fit residues: 42.9071 Evaluate side-chains 101 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1789 time to fit residues: 3.3061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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: 70.4619 > 50: distance: 44 - 66: 31.384 distance: 49 - 71: 32.822 distance: 56 - 82: 34.767 distance: 61 - 66: 29.453 distance: 62 - 91: 34.429 distance: 66 - 67: 10.469 distance: 67 - 68: 22.359 distance: 67 - 70: 4.221 distance: 68 - 71: 7.806 distance: 69 - 102: 14.692 distance: 71 - 72: 50.977 distance: 72 - 73: 39.873 distance: 72 - 75: 42.665 distance: 75 - 76: 16.811 distance: 76 - 78: 29.780 distance: 78 - 80: 10.194 distance: 79 - 81: 40.313 distance: 80 - 81: 5.509 distance: 82 - 83: 40.921 distance: 83 - 86: 39.953 distance: 84 - 91: 40.010 distance: 86 - 87: 38.362 distance: 87 - 88: 37.321 distance: 88 - 89: 39.828 distance: 91 - 92: 38.714 distance: 92 - 93: 59.865 distance: 92 - 95: 6.626 distance: 93 - 94: 31.236 distance: 93 - 102: 20.543 distance: 95 - 96: 35.419 distance: 96 - 97: 40.787 distance: 99 - 100: 37.342 distance: 99 - 101: 54.119 distance: 102 - 103: 15.270 distance: 103 - 104: 33.861 distance: 103 - 106: 69.015 distance: 104 - 105: 34.356 distance: 104 - 113: 40.161 distance: 107 - 108: 47.320 distance: 108 - 109: 45.224 distance: 109 - 110: 37.204 distance: 110 - 111: 7.388 distance: 110 - 112: 5.712 distance: 113 - 114: 24.930 distance: 114 - 115: 26.081 distance: 114 - 117: 20.229 distance: 115 - 116: 38.970 distance: 117 - 118: 48.295 distance: 122 - 123: 55.928 distance: 122 - 125: 39.662 distance: 123 - 124: 40.401 distance: 126 - 127: 38.853 distance: 128 - 130: 23.921 distance: 130 - 131: 31.816 distance: 131 - 132: 13.710 distance: 131 - 134: 11.786 distance: 132 - 138: 9.132 distance: 134 - 135: 39.564 distance: 135 - 136: 55.952 distance: 136 - 137: 57.055 distance: 138 - 139: 3.445 distance: 139 - 140: 25.191 distance: 139 - 142: 43.138 distance: 140 - 141: 22.703 distance: 140 - 149: 34.573 distance: 143 - 144: 39.349 distance: 143 - 145: 7.988 distance: 145 - 147: 17.149 distance: 146 - 148: 56.171 distance: 147 - 148: 26.136