Starting phenix.real_space_refine on Tue Mar 19 04:55:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dl2_30708/03_2024/7dl2_30708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dl2_30708/03_2024/7dl2_30708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dl2_30708/03_2024/7dl2_30708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dl2_30708/03_2024/7dl2_30708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dl2_30708/03_2024/7dl2_30708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dl2_30708/03_2024/7dl2_30708.pdb" } resolution = 4.4 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= -0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 14811 2.51 5 N 4075 2.21 5 O 4284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 864": "OE1" <-> "OE2" Residue "D ASP 872": "OD1" <-> "OD2" Residue "D GLU 878": "OE1" <-> "OE2" Residue "D TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 964": "OD1" <-> "OD2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1240": "NH1" <-> "NH2" Residue "A GLU 1243": "OE1" <-> "OE2" Residue "A PHE 1510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1573": "OE1" <-> "OE2" Residue "A TYR 1593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1688": "NH1" <-> "NH2" Residue "A PHE 1710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1729": "NH1" <-> "NH2" Residue "A TYR 1736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 439": "OD1" <-> "OD2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ARG 759": "NH1" <-> "NH2" Residue "B TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 781": "OD1" <-> "OD2" Residue "B TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 845": "OE1" <-> "OE2" Residue "B TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "B TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 899": "NH1" <-> "NH2" Residue "B PHE 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 936": "NH1" <-> "NH2" Residue "B ASP 1028": "OD1" <-> "OD2" Residue "B PHE 1050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1239": "OE1" <-> "OE2" Residue "B PHE 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1558": "OE1" <-> "OE2" Residue "B ARG 1639": "NH1" <-> "NH2" Residue "B PHE 1645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1688": "NH1" <-> "NH2" Residue "B ARG 1729": "NH1" <-> "NH2" Residue "C ARG 901": "NH1" <-> "NH2" Residue "C ARG 947": "NH1" <-> "NH2" Residue "C ARG 953": "NH1" <-> "NH2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 184": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23285 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1575 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'TRANS': 225} Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 200 Chain: "A" Number of atoms: 9016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 9016 Classifications: {'peptide': 1127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 1076} Chain breaks: 9 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7952 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 49, 'TRANS': 992} Chain breaks: 16 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 510 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 8, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 215 Chain: "C" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1558 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'TRANS': 223} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 200 Chain: "E" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2169 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 15, 'TRANS': 251} Chain: "F" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1015 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'TRANS': 202} Chain breaks: 8 Unresolved non-hydrogen bonds: 406 Unresolved non-hydrogen angles: 609 Unresolved non-hydrogen dihedrals: 203 Planarities with less than four sites: {'UNK:plan-1': 203} Unresolved non-hydrogen planarities: 203 Time building chain proxies: 11.55, per 1000 atoms: 0.50 Number of scatterers: 23285 At special positions: 0 Unit cell: (151.872, 402.732, 150.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 4284 8.00 N 4075 7.00 C 14811 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: 10.81 Conformation dependent library (CDL) restraints added in 4.0 seconds 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5996 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 5 sheets defined 73.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'D' and resid 746 through 870 removed outlier: 3.809A pdb=" N TRP D 750 " --> pdb=" O ASP D 746 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER D 836 " --> pdb=" O SER D 832 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 855 " --> pdb=" O GLN D 851 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY D 856 " --> pdb=" O LEU D 852 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 857 " --> pdb=" O LEU D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 970 removed outlier: 3.758A pdb=" N MET D 879 " --> pdb=" O LYS D 875 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N MET D 880 " --> pdb=" O GLU D 876 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS D 881 " --> pdb=" O VAL D 877 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR D 884 " --> pdb=" O MET D 880 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR D 904 " --> pdb=" O GLN D 900 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER D 914 " --> pdb=" O LEU D 910 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS D 915 " --> pdb=" O GLU D 911 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA D 917 " --> pdb=" O GLU D 913 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 944 " --> pdb=" O GLN D 940 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 947 " --> pdb=" O ALA D 943 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU D 970 " --> pdb=" O TYR D 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.897A pdb=" N ASP A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.861A pdb=" N ILE A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 231 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 288 through 300 Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 315 through 327 Proline residue: A 321 - end of helix removed outlier: 3.654A pdb=" N TYR A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 Processing helix chain 'A' and resid 359 through 377 Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 400 through 403 Processing helix chain 'A' and resid 407 through 416 removed outlier: 3.542A pdb=" N VAL A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 435 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 458 through 476 removed outlier: 3.545A pdb=" N ARG A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.981A pdb=" N ILE A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 518 removed outlier: 4.193A pdb=" N VAL A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.517A pdb=" N SER A 526 " --> pdb=" O HIS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.830A pdb=" N LEU A 545 " --> pdb=" O PRO A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 575 removed outlier: 4.493A pdb=" N ASP A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 601 Processing helix chain 'A' and resid 604 through 620 removed outlier: 4.068A pdb=" N LEU A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 700 Processing helix chain 'A' and resid 703 through 719 Proline residue: A 714 - end of helix removed outlier: 3.525A pdb=" N TYR A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 4.132A pdb=" N ILE A 723 " --> pdb=" O TYR A 719 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 removed outlier: 3.826A pdb=" N CYS A 734 " --> pdb=" O VAL A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 774 Proline residue: A 768 - end of helix Processing helix chain 'A' and resid 775 through 780 removed outlier: 4.820A pdb=" N ASN A 778 " --> pdb=" O SER A 775 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 780 " --> pdb=" O HIS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 795 Processing helix chain 'A' and resid 801 through 815 Processing helix chain 'A' and resid 815 through 830 removed outlier: 4.304A pdb=" N LYS A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Proline residue: A 824 - end of helix Processing helix chain 'A' and resid 839 through 852 removed outlier: 3.557A pdb=" N LEU A 843 " --> pdb=" O MET A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 873 Processing helix chain 'A' and resid 874 through 877 removed outlier: 3.986A pdb=" N ASN A 877 " --> pdb=" O PRO A 874 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 874 through 877' Processing helix chain 'A' and resid 882 through 900 Processing helix chain 'A' and resid 907 through 920 removed outlier: 3.954A pdb=" N PHE A 911 " --> pdb=" O ASP A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1034 Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1076 through 1082 Processing helix chain 'A' and resid 1182 through 1185 removed outlier: 3.920A pdb=" N ALA A1185 " --> pdb=" O ASN A1182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1182 through 1185' Processing helix chain 'A' and resid 1186 through 1193 removed outlier: 3.761A pdb=" N GLY A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1239 removed outlier: 3.561A pdb=" N ALA A1237 " --> pdb=" O ASN A1233 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A1239 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1505 removed outlier: 4.038A pdb=" N PHE A1501 " --> pdb=" O PRO A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1537 Processing helix chain 'A' and resid 1568 through 1577 removed outlier: 3.543A pdb=" N GLY A1577 " --> pdb=" O GLU A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1643 Processing helix chain 'A' and resid 1658 through 1662 Processing helix chain 'A' and resid 1707 through 1728 Processing helix chain 'A' and resid 1738 through 1755 removed outlier: 3.723A pdb=" N CYS A1755 " --> pdb=" O ARG A1751 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.693A pdb=" N VAL B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.636A pdb=" N LEU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 248 Processing helix chain 'B' and resid 265 through 273 Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 318 through 328 removed outlier: 4.320A pdb=" N SER B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.653A pdb=" N SER B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 377 Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 409 through 418 removed outlier: 3.983A pdb=" N ARG B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 434 Processing helix chain 'B' and resid 443 through 451 removed outlier: 4.384A pdb=" N ALA B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.714A pdb=" N ARG B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 5.802A pdb=" N GLU B 482 " --> pdb=" O GLN B 478 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN B 486 " --> pdb=" O GLU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 517 removed outlier: 3.703A pdb=" N GLU B 517 " --> pdb=" O VAL B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 535 removed outlier: 3.630A pdb=" N SER B 526 " --> pdb=" O HIS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 574 removed outlier: 4.566A pdb=" N ALA B 552 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 576 No H-bonds generated for 'chain 'B' and resid 575 through 576' Processing helix chain 'B' and resid 577 through 578 No H-bonds generated for 'chain 'B' and resid 577 through 578' Processing helix chain 'B' and resid 579 through 600 removed outlier: 3.922A pdb=" N ALA B 583 " --> pdb=" O PRO B 579 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 687 through 699 removed outlier: 3.755A pdb=" N ARG B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 719 Proline residue: B 714 - end of helix Processing helix chain 'B' and resid 721 through 725 removed outlier: 3.653A pdb=" N PHE B 724 " --> pdb=" O VAL B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 740 removed outlier: 3.790A pdb=" N LEU B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 774 Proline residue: B 768 - end of helix Processing helix chain 'B' and resid 781 through 797 removed outlier: 4.282A pdb=" N ILE B 797 " --> pdb=" O GLU B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 815 Processing helix chain 'B' and resid 815 through 831 removed outlier: 3.544A pdb=" N ILE B 819 " --> pdb=" O MET B 815 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Proline residue: B 824 - end of helix Processing helix chain 'B' and resid 839 through 852 removed outlier: 3.696A pdb=" N LEU B 844 " --> pdb=" O ALA B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 873 removed outlier: 3.867A pdb=" N TYR B 865 " --> pdb=" O ALA B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 877 Processing helix chain 'B' and resid 882 through 900 Processing helix chain 'B' and resid 907 through 918 removed outlier: 4.674A pdb=" N PHE B 911 " --> pdb=" O ASP B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1034 Processing helix chain 'B' and resid 1045 through 1053 Processing helix chain 'B' and resid 1074 through 1082 Processing helix chain 'B' and resid 1181 through 1185 Processing helix chain 'B' and resid 1186 through 1192 removed outlier: 4.026A pdb=" N THR B1191 " --> pdb=" O VAL B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1228 through 1242 Processing helix chain 'B' and resid 1497 through 1505 removed outlier: 3.602A pdb=" N PHE B1501 " --> pdb=" O PRO B1497 " (cutoff:3.500A) Processing helix chain 'B' and resid 1512 through 1516 Processing helix chain 'B' and resid 1524 through 1537 removed outlier: 4.121A pdb=" N GLU B1528 " --> pdb=" O SER B1524 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B1537 " --> pdb=" O LEU B1533 " (cutoff:3.500A) Processing helix chain 'B' and resid 1568 through 1579 removed outlier: 4.093A pdb=" N GLY B1579 " --> pdb=" O LEU B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1637 through 1644 removed outlier: 3.715A pdb=" N ASN B1643 " --> pdb=" O ARG B1639 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B1644 " --> pdb=" O HIS B1640 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1662 Processing helix chain 'B' and resid 1704 through 1706 No H-bonds generated for 'chain 'B' and resid 1704 through 1706' Processing helix chain 'B' and resid 1707 through 1730 Processing helix chain 'B' and resid 1738 through 1755 Processing helix chain 'C' and resid 747 through 841 removed outlier: 3.631A pdb=" N GLU C 766 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 767 " --> pdb=" O GLN C 763 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 809 " --> pdb=" O ASN C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 871 removed outlier: 3.802A pdb=" N ASN C 849 " --> pdb=" O MET C 845 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 850 " --> pdb=" O GLU C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 875 through 967 removed outlier: 3.736A pdb=" N GLU C 887 " --> pdb=" O ALA C 883 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS C 890 " --> pdb=" O LYS C 886 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER C 905 " --> pdb=" O ARG C 901 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 907 " --> pdb=" O ASP C 903 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 32 Processing helix chain 'E' and resid 39 through 49 Processing helix chain 'E' and resid 52 through 64 removed outlier: 4.257A pdb=" N ALA E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU E 58 " --> pdb=" O MET E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 73 through 95 removed outlier: 3.609A pdb=" N VAL E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 116 removed outlier: 3.969A pdb=" N ARG E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 145 Processing helix chain 'E' and resid 147 through 165 Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'E' and resid 172 through 183 removed outlier: 3.606A pdb=" N ALA E 176 " --> pdb=" O GLN E 172 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 196 removed outlier: 3.527A pdb=" N HIS E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 201 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.853A pdb=" N LEU E 205 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 219 Processing helix chain 'E' and resid 220 through 229 removed outlier: 3.746A pdb=" N TRP E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 246 removed outlier: 3.513A pdb=" N PHE E 237 " --> pdb=" O LYS E 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 252 Processing helix chain 'E' and resid 255 through 265 Processing helix chain 'E' and resid 270 through 286 removed outlier: 3.767A pdb=" N ASP E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 34 Processing helix chain 'F' and resid 41 through 51 removed outlier: 4.016A pdb=" N UNK F 51 " --> pdb=" O UNK F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 removed outlier: 3.869A pdb=" N UNK F 60 " --> pdb=" O UNK F 56 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N UNK F 65 " --> pdb=" O UNK F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 80 removed outlier: 3.717A pdb=" N UNK F 80 " --> pdb=" O UNK F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'F' and resid 123 through 133 Processing helix chain 'F' and resid 143 through 156 Processing helix chain 'F' and resid 163 through 170 removed outlier: 4.149A pdb=" N UNK F 167 " --> pdb=" O UNK F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 191 Processing helix chain 'F' and resid 196 through 209 removed outlier: 3.916A pdb=" N UNK F 200 " --> pdb=" O UNK F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 231 through 237 removed outlier: 4.113A pdb=" N UNK F 237 " --> pdb=" O UNK F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 260 removed outlier: 3.520A pdb=" N UNK F 249 " --> pdb=" O UNK F 245 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N UNK F 260 " --> pdb=" O UNK F 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 622 through 623 Processing sheet with id=AA2, first strand: chain 'A' and resid 1518 through 1519 removed outlier: 3.947A pdb=" N LEU A1209 " --> pdb=" O SER B1211 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B1211 " --> pdb=" O LEU A1209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1609 through 1611 removed outlier: 6.248A pdb=" N ASP A1541 " --> pdb=" O GLN A1616 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL A1618 " --> pdb=" O ASP A1541 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS A1543 " --> pdb=" O VAL A1618 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N HIS A1620 " --> pdb=" O HIS A1543 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE A1545 " --> pdb=" O HIS A1620 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL A1646 " --> pdb=" O LYS A1544 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER A1647 " --> pdb=" O VAL A1671 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A1673 " --> pdb=" O SER A1647 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A1649 " --> pdb=" O VAL A1673 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1547 through 1549 removed outlier: 3.819A pdb=" N TYR B1650 " --> pdb=" O LEU B1548 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B1671 " --> pdb=" O SER B1647 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1609 through 1610 1510 hydrogen bonds defined for protein. 4440 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: 8.39 Time building geometry restraints manager: 11.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6748 1.33 - 1.45: 3650 1.45 - 1.58: 13114 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 23686 Sorted by residual: bond pdb=" N THR E 102 " pdb=" CA THR E 102 " ideal model delta sigma weight residual 1.455 1.489 -0.033 7.00e-03 2.04e+04 2.29e+01 bond pdb=" C GLN B1532 " pdb=" O GLN B1532 " ideal model delta sigma weight residual 1.236 1.275 -0.039 1.15e-02 7.56e+03 1.14e+01 bond pdb=" N GLN B1536 " pdb=" CA GLN B1536 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" N VAL B1646 " pdb=" CA VAL B1646 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.15e-02 7.56e+03 1.03e+01 bond pdb=" N GLN B1532 " pdb=" CA GLN B1532 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.17e-02 7.31e+03 9.93e+00 ... (remaining 23681 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.92: 450 105.92 - 113.01: 13277 113.01 - 120.11: 8481 120.11 - 127.20: 9717 127.20 - 134.30: 233 Bond angle restraints: 32158 Sorted by residual: angle pdb=" N PRO B 232 " pdb=" CA PRO B 232 " pdb=" CB PRO B 232 " ideal model delta sigma weight residual 103.00 110.49 -7.49 1.10e+00 8.26e-01 4.63e+01 angle pdb=" N PRO B 131 " pdb=" CA PRO B 131 " pdb=" CB PRO B 131 " ideal model delta sigma weight residual 103.39 110.35 -6.96 1.08e+00 8.57e-01 4.16e+01 angle pdb=" O ASP B1613 " pdb=" C ASP B1613 " pdb=" N ILE B1614 " ideal model delta sigma weight residual 122.09 115.67 6.42 1.04e+00 9.25e-01 3.81e+01 angle pdb=" N PRO B 290 " pdb=" CA PRO B 290 " pdb=" CB PRO B 290 " ideal model delta sigma weight residual 103.39 110.03 -6.64 1.08e+00 8.57e-01 3.78e+01 angle pdb=" N PRO B 237 " pdb=" CA PRO B 237 " pdb=" CB PRO B 237 " ideal model delta sigma weight residual 103.44 110.18 -6.74 1.12e+00 7.97e-01 3.63e+01 ... (remaining 32153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 13041 17.64 - 35.28: 1122 35.28 - 52.92: 201 52.92 - 70.55: 29 70.55 - 88.19: 15 Dihedral angle restraints: 14408 sinusoidal: 5272 harmonic: 9136 Sorted by residual: dihedral pdb=" CA ASP A1656 " pdb=" C ASP A1656 " pdb=" N PHE A1657 " pdb=" CA PHE A1657 " ideal model delta harmonic sigma weight residual -180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ASN A1731 " pdb=" C ASN A1731 " pdb=" N PRO A1732 " pdb=" CA PRO A1732 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C THR D 874 " pdb=" N THR D 874 " pdb=" CA THR D 874 " pdb=" CB THR D 874 " ideal model delta harmonic sigma weight residual -122.00 -133.30 11.30 0 2.50e+00 1.60e-01 2.04e+01 ... (remaining 14405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3318 0.079 - 0.158: 421 0.158 - 0.237: 73 0.237 - 0.316: 4 0.316 - 0.395: 3 Chirality restraints: 3819 Sorted by residual: chirality pdb=" CA LYS D 881 " pdb=" N LYS D 881 " pdb=" C LYS D 881 " pdb=" CB LYS D 881 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA GLN D 844 " pdb=" N GLN D 844 " pdb=" C GLN D 844 " pdb=" CB GLN D 844 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA THR D 874 " pdb=" N THR D 874 " pdb=" C THR D 874 " pdb=" CB THR D 874 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 3816 not shown) Planarity restraints: 4110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 868 " 0.020 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C ASN D 868 " -0.074 2.00e-02 2.50e+03 pdb=" O ASN D 868 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS D 869 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 776 " -0.039 2.00e-02 2.50e+03 2.78e-02 1.55e+01 pdb=" CG TYR B 776 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 776 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 776 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 776 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR B 776 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 776 " 0.029 2.00e-02 2.50e+03 pdb=" OH TYR B 776 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B1613 " -0.021 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ASP B1613 " 0.068 2.00e-02 2.50e+03 pdb=" O ASP B1613 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE B1614 " -0.023 2.00e-02 2.50e+03 ... (remaining 4107 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2777 2.74 - 3.28: 28541 3.28 - 3.82: 40053 3.82 - 4.36: 46607 4.36 - 4.90: 71843 Nonbonded interactions: 189821 Sorted by model distance: nonbonded pdb=" N GLU E 217 " pdb=" OE1 GLU E 217 " model vdw 2.202 2.520 nonbonded pdb=" O TYR A 553 " pdb=" OG SER A 556 " model vdw 2.205 2.440 nonbonded pdb=" O CYS A 206 " pdb=" OG1 THR A 209 " model vdw 2.210 2.440 nonbonded pdb=" O LEU A 713 " pdb=" OG SER A 716 " model vdw 2.210 2.440 nonbonded pdb=" O GLN B1229 " pdb=" OG SER B1232 " model vdw 2.211 2.440 ... (remaining 189816 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 127 through 141 and (name N or name CA or name C or name \ O or name CB )) or (resid 160 through 170 and (name N or name CA or name C or na \ me O or name CB )) or resid 171 or (resid 172 through 174 and (name N or name CA \ or name C or name O or name CB )) or (resid 185 through 200 and (name N or name \ CA or name C or name O or name CB )) or (resid 211 through 225 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 232 through 250 and (name N o \ r name CA or name C or name O or name CB )) or (resid 262 through 264 and (name \ N or name CA or name C or name O or name CB )) or resid 265 or (resid 266 throug \ h 268 and (name N or name CA or name C or name O or name CB )) or resid 269 or ( \ resid 270 through 276 and (name N or name CA or name C or name O or name CB )) o \ r (resid 281 through 293 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 294 through 299 and (name N or name CA or name C or name O or name C \ B )) or resid 300 or (resid 301 through 304 and (name N or name CA or name C or \ name O or name CB )) or resid 305 or resid 316 through 400 or resid 407 through \ 623 or resid 685 through 748 or resid 758 through 1242 or resid 1494 through 175 \ 5)) selection = (chain 'B' and (resid 127 through 936 or resid 1015 through 1082 or resid 1182 t \ hrough 1221 or resid 1230 through 1242 or resid 1494 through 1755)) } ncs_group { reference = (chain 'C' and ((resid 746 through 840 and (name N or name CA or name C or name \ O or name CB )) or resid 841 through 969)) selection = (chain 'D' and resid 746 through 969) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.260 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: 30.840 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 62.440 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.006 0.042 23686 Z= 0.386 Angle : 0.883 9.634 32158 Z= 0.586 Chirality : 0.056 0.395 3819 Planarity : 0.005 0.053 4110 Dihedral : 13.739 88.192 8412 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 35.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.08 % Favored : 89.77 % Rotamer: Outliers : 1.11 % Allowed : 9.17 % Favored : 89.71 % Cbeta Deviations : 0.03 % 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: -3.66 (0.14), residues: 2826 helix: -1.53 (0.11), residues: 1774 sheet: -3.35 (0.34), residues: 148 loop : -3.93 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 304 HIS 0.009 0.001 HIS A 593 PHE 0.024 0.002 PHE B 860 TYR 0.050 0.002 TYR B 776 ARG 0.007 0.001 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 954 ILE cc_start: 0.9365 (mt) cc_final: 0.8089 (mt) REVERT: D 958 PHE cc_start: 0.8692 (m-10) cc_final: 0.8454 (m-80) REVERT: A 267 HIS cc_start: 0.8653 (t-90) cc_final: 0.8195 (t-170) REVERT: A 276 MET cc_start: 0.9094 (tpt) cc_final: 0.8695 (tpp) REVERT: A 278 HIS cc_start: 0.8781 (m90) cc_final: 0.8564 (m90) REVERT: A 301 MET cc_start: 0.8161 (tpp) cc_final: 0.7763 (tpp) REVERT: A 449 MET cc_start: 0.8829 (tpt) cc_final: 0.8517 (ttp) REVERT: A 1022 LEU cc_start: 0.9374 (mm) cc_final: 0.9095 (mt) REVERT: A 1210 MET cc_start: 0.9154 (mmt) cc_final: 0.8785 (mmp) REVERT: B 740 MET cc_start: 0.9095 (ptt) cc_final: 0.8867 (mtm) REVERT: B 1029 MET cc_start: 0.8958 (tmm) cc_final: 0.8736 (tmm) REVERT: B 1030 MET cc_start: 0.9146 (mtm) cc_final: 0.8548 (mtp) REVERT: C 931 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8637 (mm-30) REVERT: C 954 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.8895 (tp) outliers start: 26 outliers final: 12 residues processed: 181 average time/residue: 0.3730 time to fit residues: 106.3901 Evaluate side-chains 130 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 156 optimal weight: 0.4980 chunk 123 optimal weight: 0.8980 chunk 239 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN D 897 GLN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 HIS ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 940 GLN D 956 GLN A 182 ASN A 248 ASN A 331 ASN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS A 883 GLN A 891 HIS A1064 ASN ** A1588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1640 HIS A1726 HIS B 363 ASN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS B 699 GLN ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1182 ASN B1503 GLN ** B1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1651 ASN ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 113 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23686 Z= 0.215 Angle : 0.680 9.729 32158 Z= 0.346 Chirality : 0.040 0.203 3819 Planarity : 0.005 0.067 4110 Dihedral : 5.064 26.169 3289 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.30 % Allowed : 6.47 % Favored : 93.23 % 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: -1.83 (0.15), residues: 2826 helix: -0.13 (0.12), residues: 1837 sheet: -2.59 (0.37), residues: 154 loop : -3.34 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 441 HIS 0.010 0.001 HIS D 894 PHE 0.035 0.002 PHE B 860 TYR 0.026 0.002 TYR C 884 ARG 0.011 0.001 ARG C 953 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8370 (t0) REVERT: A 301 MET cc_start: 0.8064 (tpp) cc_final: 0.7674 (tpp) REVERT: A 1022 LEU cc_start: 0.9301 (mm) cc_final: 0.9027 (mt) REVERT: A 1721 MET cc_start: 0.9011 (mtp) cc_final: 0.8620 (mmm) REVERT: B 449 MET cc_start: 0.8607 (ppp) cc_final: 0.8356 (ppp) REVERT: B 845 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8821 (mt-10) REVERT: B 1030 MET cc_start: 0.8951 (mtm) cc_final: 0.8306 (mtm) outliers start: 7 outliers final: 1 residues processed: 150 average time/residue: 0.3545 time to fit residues: 85.2969 Evaluate side-chains 113 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 231 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 276 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1515 ASN ** A1588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 HIS B1503 GLN ** B1532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 GLN ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 900 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23686 Z= 0.192 Angle : 0.638 8.902 32158 Z= 0.324 Chirality : 0.039 0.347 3819 Planarity : 0.004 0.052 4110 Dihedral : 4.855 25.016 3289 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % 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: -0.99 (0.16), residues: 2826 helix: 0.55 (0.12), residues: 1835 sheet: -2.11 (0.38), residues: 152 loop : -3.10 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.008 0.001 HIS A1506 PHE 0.032 0.002 PHE B 860 TYR 0.043 0.002 TYR D 966 ARG 0.006 0.000 ARG D 947 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 884 TYR cc_start: 0.8230 (t80) cc_final: 0.7968 (t80) REVERT: D 954 ILE cc_start: 0.9496 (mt) cc_final: 0.8309 (mt) REVERT: A 301 MET cc_start: 0.7976 (tpp) cc_final: 0.7662 (tpp) REVERT: A 466 LEU cc_start: 0.9601 (tp) cc_final: 0.9362 (tp) REVERT: A 1022 LEU cc_start: 0.9288 (mm) cc_final: 0.9038 (mt) REVERT: A 1030 MET cc_start: 0.8344 (mmp) cc_final: 0.7055 (mmm) REVERT: A 1721 MET cc_start: 0.8944 (mtp) cc_final: 0.8567 (mmm) REVERT: B 449 MET cc_start: 0.8640 (ppp) cc_final: 0.8368 (ppp) REVERT: B 845 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8846 (mt-10) REVERT: B 1030 MET cc_start: 0.8966 (mtm) cc_final: 0.8215 (mtm) REVERT: B 1613 ASP cc_start: 0.9027 (p0) cc_final: 0.8819 (p0) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.3883 time to fit residues: 89.5901 Evaluate side-chains 109 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 chunk 144 optimal weight: 40.0000 chunk 30 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 279 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 GLN ** A1588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 23686 Z= 0.392 Angle : 0.746 10.583 32158 Z= 0.387 Chirality : 0.041 0.190 3819 Planarity : 0.005 0.072 4110 Dihedral : 5.105 26.443 3289 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % 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: -1.15 (0.16), residues: 2826 helix: 0.42 (0.12), residues: 1841 sheet: -2.17 (0.38), residues: 153 loop : -3.16 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 703 HIS 0.020 0.002 HIS A 278 PHE 0.027 0.002 PHE A 860 TYR 0.038 0.002 TYR D 966 ARG 0.012 0.001 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 884 TYR cc_start: 0.8219 (t80) cc_final: 0.7940 (t80) REVERT: A 276 MET cc_start: 0.8908 (tpt) cc_final: 0.8665 (tpp) REVERT: A 301 MET cc_start: 0.8141 (tpp) cc_final: 0.7776 (tpp) REVERT: A 1022 LEU cc_start: 0.9377 (mm) cc_final: 0.9133 (mt) REVERT: A 1210 MET cc_start: 0.9021 (mmp) cc_final: 0.8717 (mmp) REVERT: A 1721 MET cc_start: 0.9028 (mtp) cc_final: 0.8706 (mmm) REVERT: B 449 MET cc_start: 0.8721 (ppp) cc_final: 0.8462 (ppp) REVERT: B 1030 MET cc_start: 0.8777 (mtm) cc_final: 0.7817 (mtm) outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.3092 time to fit residues: 65.0230 Evaluate side-chains 98 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.9980 chunk 167 optimal weight: 0.0030 chunk 4 optimal weight: 40.0000 chunk 220 optimal weight: 0.4980 chunk 122 optimal weight: 0.0970 chunk 252 optimal weight: 0.0980 chunk 204 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 GLN A 267 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 849 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23686 Z= 0.179 Angle : 0.640 10.270 32158 Z= 0.320 Chirality : 0.039 0.205 3819 Planarity : 0.004 0.081 4110 Dihedral : 4.790 24.939 3289 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: -0.51 (0.16), residues: 2826 helix: 0.90 (0.12), residues: 1839 sheet: -1.89 (0.39), residues: 152 loop : -2.88 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 441 HIS 0.014 0.001 HIS A 278 PHE 0.035 0.002 PHE B 860 TYR 0.015 0.001 TYR A 779 ARG 0.011 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 884 TYR cc_start: 0.7976 (t80) cc_final: 0.7751 (t80) REVERT: D 954 ILE cc_start: 0.9604 (mt) cc_final: 0.9074 (mt) REVERT: D 958 PHE cc_start: 0.9126 (m-80) cc_final: 0.8689 (m-80) REVERT: A 301 MET cc_start: 0.8090 (tpp) cc_final: 0.7586 (tpp) REVERT: A 392 GLU cc_start: 0.8657 (tp30) cc_final: 0.8450 (tp30) REVERT: A 1022 LEU cc_start: 0.9252 (mm) cc_final: 0.9045 (mt) REVERT: A 1210 MET cc_start: 0.8974 (mmp) cc_final: 0.8423 (mmp) REVERT: A 1721 MET cc_start: 0.8921 (mtp) cc_final: 0.8532 (mmm) REVERT: B 449 MET cc_start: 0.8645 (ppp) cc_final: 0.8399 (ppp) REVERT: B 535 MET cc_start: 0.8663 (ptt) cc_final: 0.8459 (ptp) REVERT: B 740 MET cc_start: 0.9318 (ptp) cc_final: 0.9111 (ptt) REVERT: B 788 MET cc_start: 0.8664 (ptp) cc_final: 0.8012 (ptp) REVERT: B 845 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8713 (mt-10) REVERT: B 1030 MET cc_start: 0.8847 (mtm) cc_final: 0.8175 (mtm) REVERT: B 1613 ASP cc_start: 0.9017 (p0) cc_final: 0.8751 (p0) REVERT: B 1691 MET cc_start: 0.7478 (ptp) cc_final: 0.7237 (ptp) REVERT: E 251 MET cc_start: 0.7587 (mmp) cc_final: 0.7308 (mmt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3350 time to fit residues: 77.4612 Evaluate side-chains 114 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.9980 chunk 266 optimal weight: 0.0670 chunk 58 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 296 optimal weight: 20.0000 chunk 245 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23686 Z= 0.173 Angle : 0.621 11.651 32158 Z= 0.311 Chirality : 0.039 0.379 3819 Planarity : 0.005 0.128 4110 Dihedral : 4.613 23.719 3289 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: -0.26 (0.16), residues: 2826 helix: 1.09 (0.12), residues: 1848 sheet: -1.75 (0.40), residues: 152 loop : -2.84 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 441 HIS 0.011 0.001 HIS A 278 PHE 0.032 0.001 PHE B 860 TYR 0.015 0.001 TYR D 966 ARG 0.014 0.000 ARG D 953 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 884 TYR cc_start: 0.7955 (t80) cc_final: 0.7745 (t80) REVERT: D 954 ILE cc_start: 0.9509 (mt) cc_final: 0.8811 (mt) REVERT: D 958 PHE cc_start: 0.9029 (m-80) cc_final: 0.8583 (m-80) REVERT: A 301 MET cc_start: 0.8098 (tpp) cc_final: 0.7624 (tpp) REVERT: A 466 LEU cc_start: 0.9598 (tp) cc_final: 0.9387 (tp) REVERT: A 510 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8320 (mm110) REVERT: A 1022 LEU cc_start: 0.9271 (mm) cc_final: 0.9045 (mt) REVERT: A 1721 MET cc_start: 0.8893 (mtp) cc_final: 0.8573 (mmm) REVERT: B 449 MET cc_start: 0.8640 (ppp) cc_final: 0.8414 (ppp) REVERT: B 740 MET cc_start: 0.9295 (ptp) cc_final: 0.9066 (ptt) REVERT: B 788 MET cc_start: 0.8689 (ptp) cc_final: 0.8103 (ptp) REVERT: B 845 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8769 (mt-10) REVERT: B 1030 MET cc_start: 0.8844 (mtm) cc_final: 0.8126 (mtm) REVERT: B 1613 ASP cc_start: 0.8917 (p0) cc_final: 0.8296 (p0) REVERT: B 1691 MET cc_start: 0.7449 (ptp) cc_final: 0.7220 (ptp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3314 time to fit residues: 75.8171 Evaluate side-chains 111 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 168 optimal weight: 0.9990 chunk 216 optimal weight: 0.3980 chunk 167 optimal weight: 20.0000 chunk 249 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 294 optimal weight: 9.9990 chunk 184 optimal weight: 0.4980 chunk 179 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1554 GLN ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23686 Z= 0.171 Angle : 0.620 9.700 32158 Z= 0.311 Chirality : 0.039 0.418 3819 Planarity : 0.004 0.090 4110 Dihedral : 4.530 22.980 3289 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -0.09 (0.16), residues: 2826 helix: 1.20 (0.12), residues: 1857 sheet: -1.74 (0.40), residues: 158 loop : -2.75 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 441 HIS 0.014 0.001 HIS A 278 PHE 0.031 0.001 PHE B 860 TYR 0.014 0.001 TYR A 779 ARG 0.012 0.000 ARG D 953 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 954 ILE cc_start: 0.9523 (mt) cc_final: 0.8795 (mt) REVERT: D 958 PHE cc_start: 0.8945 (m-80) cc_final: 0.8628 (m-80) REVERT: A 301 MET cc_start: 0.8011 (tpp) cc_final: 0.7598 (tpp) REVERT: A 510 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8365 (mm110) REVERT: A 1022 LEU cc_start: 0.9266 (mm) cc_final: 0.9030 (mt) REVERT: B 449 MET cc_start: 0.8657 (ppp) cc_final: 0.8431 (ppp) REVERT: B 740 MET cc_start: 0.9310 (ptp) cc_final: 0.9102 (ptt) REVERT: B 788 MET cc_start: 0.8645 (ptp) cc_final: 0.8037 (ptp) REVERT: B 845 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8762 (mt-10) REVERT: B 1030 MET cc_start: 0.8843 (mtm) cc_final: 0.8105 (mtm) REVERT: B 1691 MET cc_start: 0.7355 (ptp) cc_final: 0.7146 (ptp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3345 time to fit residues: 75.7639 Evaluate side-chains 113 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 145 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23686 Z= 0.198 Angle : 0.618 9.116 32158 Z= 0.313 Chirality : 0.039 0.341 3819 Planarity : 0.004 0.071 4110 Dihedral : 4.496 23.079 3289 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: 0.00 (0.16), residues: 2826 helix: 1.24 (0.12), residues: 1860 sheet: -1.53 (0.40), residues: 155 loop : -2.68 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 441 HIS 0.006 0.001 HIS A1506 PHE 0.042 0.002 PHE A 298 TYR 0.020 0.001 TYR D 966 ARG 0.010 0.000 ARG D 953 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 884 TYR cc_start: 0.7801 (t80) cc_final: 0.7589 (t80) REVERT: D 954 ILE cc_start: 0.9515 (mt) cc_final: 0.8707 (mt) REVERT: D 958 PHE cc_start: 0.8938 (m-80) cc_final: 0.8600 (m-80) REVERT: A 301 MET cc_start: 0.7931 (tpp) cc_final: 0.7603 (tpp) REVERT: A 466 LEU cc_start: 0.9574 (tp) cc_final: 0.9372 (tp) REVERT: A 510 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8381 (mm110) REVERT: A 1022 LEU cc_start: 0.9277 (mm) cc_final: 0.9041 (mt) REVERT: B 449 MET cc_start: 0.8693 (ppp) cc_final: 0.8452 (ppp) REVERT: B 845 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8749 (mt-10) REVERT: B 1030 MET cc_start: 0.8846 (mtm) cc_final: 0.8101 (mtm) REVERT: B 1691 MET cc_start: 0.7422 (ptp) cc_final: 0.7199 (ptp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3411 time to fit residues: 75.4322 Evaluate side-chains 108 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 180 optimal weight: 0.0000 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 GLN A1727 HIS ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23686 Z= 0.169 Angle : 0.625 9.612 32158 Z= 0.312 Chirality : 0.039 0.334 3819 Planarity : 0.004 0.061 4110 Dihedral : 4.418 22.396 3289 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.14 (0.17), residues: 2826 helix: 1.34 (0.12), residues: 1862 sheet: -1.37 (0.41), residues: 155 loop : -2.64 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 441 HIS 0.008 0.001 HIS A1506 PHE 0.038 0.001 PHE A 298 TYR 0.045 0.001 TYR D 966 ARG 0.008 0.000 ARG D 953 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 884 TYR cc_start: 0.7868 (t80) cc_final: 0.7635 (t80) REVERT: D 954 ILE cc_start: 0.9482 (mt) cc_final: 0.8578 (mt) REVERT: D 958 PHE cc_start: 0.8854 (m-80) cc_final: 0.8527 (m-80) REVERT: A 301 MET cc_start: 0.7874 (tpp) cc_final: 0.7600 (tpp) REVERT: A 466 LEU cc_start: 0.9632 (tp) cc_final: 0.9316 (mt) REVERT: A 510 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8286 (mm110) REVERT: A 888 LEU cc_start: 0.8985 (mt) cc_final: 0.8727 (mm) REVERT: A 1022 LEU cc_start: 0.9241 (mm) cc_final: 0.9012 (mt) REVERT: A 1721 MET cc_start: 0.8923 (mtp) cc_final: 0.8307 (mmm) REVERT: B 449 MET cc_start: 0.8677 (ppp) cc_final: 0.8453 (ppp) REVERT: B 845 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8768 (mt-10) REVERT: B 1030 MET cc_start: 0.8818 (mtm) cc_final: 0.8076 (mtm) REVERT: B 1691 MET cc_start: 0.7344 (ptp) cc_final: 0.7133 (ptp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3332 time to fit residues: 75.0221 Evaluate side-chains 114 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 9.9990 chunk 280 optimal weight: 0.9980 chunk 242 optimal weight: 30.0000 chunk 25 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 192 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23686 Z= 0.250 Angle : 0.657 8.938 32158 Z= 0.335 Chirality : 0.040 0.287 3819 Planarity : 0.004 0.060 4110 Dihedral : 4.543 23.381 3289 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 0.04 (0.16), residues: 2826 helix: 1.25 (0.12), residues: 1871 sheet: -1.46 (0.41), residues: 155 loop : -2.69 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1208 HIS 0.006 0.001 HIS A 593 PHE 0.030 0.002 PHE A 298 TYR 0.017 0.002 TYR B 429 ARG 0.009 0.001 ARG D 953 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 884 TYR cc_start: 0.7821 (t80) cc_final: 0.7568 (t80) REVERT: D 954 ILE cc_start: 0.9504 (mt) cc_final: 0.8845 (mt) REVERT: D 958 PHE cc_start: 0.8950 (m-80) cc_final: 0.8624 (m-10) REVERT: A 301 MET cc_start: 0.7858 (tpp) cc_final: 0.7602 (tpp) REVERT: A 466 LEU cc_start: 0.9603 (tp) cc_final: 0.9377 (tt) REVERT: A 510 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8313 (mm110) REVERT: A 888 LEU cc_start: 0.9076 (mt) cc_final: 0.8833 (mm) REVERT: A 1022 LEU cc_start: 0.9308 (mm) cc_final: 0.9105 (mt) REVERT: A 1029 MET cc_start: 0.8885 (tmm) cc_final: 0.8371 (tmm) REVERT: A 1030 MET cc_start: 0.8660 (mmp) cc_final: 0.7192 (mmm) REVERT: A 1721 MET cc_start: 0.8996 (mtp) cc_final: 0.8431 (mmm) REVERT: B 449 MET cc_start: 0.8742 (ppp) cc_final: 0.8506 (ppp) REVERT: B 845 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8780 (mt-10) REVERT: B 1030 MET cc_start: 0.8852 (mtm) cc_final: 0.8083 (mtm) REVERT: B 1691 MET cc_start: 0.7525 (ptp) cc_final: 0.7282 (ptp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3433 time to fit residues: 74.3731 Evaluate side-chains 109 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 223 optimal weight: 0.0000 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 243 optimal weight: 50.0000 chunk 101 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 213 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.049085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.035358 restraints weight = 222892.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036321 restraints weight = 126200.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.036946 restraints weight = 86819.792| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23686 Z= 0.174 Angle : 0.628 10.915 32158 Z= 0.314 Chirality : 0.039 0.277 3819 Planarity : 0.004 0.057 4110 Dihedral : 4.450 22.769 3289 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 0.19 (0.17), residues: 2826 helix: 1.37 (0.12), residues: 1872 sheet: -1.50 (0.41), residues: 158 loop : -2.62 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 441 HIS 0.008 0.001 HIS A1506 PHE 0.030 0.001 PHE B 860 TYR 0.024 0.001 TYR D 966 ARG 0.007 0.000 ARG D 953 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3828.94 seconds wall clock time: 72 minutes 4.46 seconds (4324.46 seconds total)