Starting phenix.real_space_refine on Fri Dec 8 21:24:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wby_21601/12_2023/6wby_21601.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wby_21601/12_2023/6wby_21601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wby_21601/12_2023/6wby_21601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wby_21601/12_2023/6wby_21601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wby_21601/12_2023/6wby_21601.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wby_21601/12_2023/6wby_21601.pdb" } resolution = 3.4 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= 1.000 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 19 5.16 5 C 5848 2.51 5 N 1609 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ASP 567": "OD1" <-> "OD2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ASP 673": "OD1" <-> "OD2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A GLU 905": "OE1" <-> "OE2" Residue "A ARG 911": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A ARG 936": "NH1" <-> "NH2" Residue "A ASP 937": "OD1" <-> "OD2" Residue "A ASP 955": "OD1" <-> "OD2" Residue "A ASP 1022": "OD1" <-> "OD2" Residue "A ARG 1027": "NH1" <-> "NH2" Residue "A ASP 1030": "OD1" <-> "OD2" Residue "A ARG 1061": "NH1" <-> "NH2" Residue "A PHE 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1140": "OD1" <-> "OD2" Residue "A ASP 1164": "OD1" <-> "OD2" Residue "A ARG 1204": "NH1" <-> "NH2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "A ASP 1244": "OD1" <-> "OD2" Residue "A PHE 1252": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9156 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9156 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1252, 9146 Unusual residues: {' CA': 2} Classifications: {'peptide': 1250, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 104, 'TRANS': 1144, None: 2} Not linked: pdbres="VAL A1388 " pdbres=" CA A2001 " Not linked: pdbres=" CA A2001 " pdbres=" CA A2002 " Chain breaks: 13 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 133 Conformer: "B" Number of residues, atoms: 1252, 9146 Unusual residues: {' CA': 2} Classifications: {'peptide': 1250, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 104, 'TRANS': 1144, None: 2} Not linked: pdbres="VAL A1388 " pdbres=" CA A2001 " Not linked: pdbres=" CA A2001 " pdbres=" CA A2002 " Chain breaks: 13 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 133 bond proxies already assigned to first conformer: 9353 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 550 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 550 " occ=0.50 Time building chain proxies: 9.60, per 1000 atoms: 1.05 Number of scatterers: 9156 At special positions: 0 Unit cell: (128.321, 89.082, 96.5055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 19 16.00 O 1678 8.00 N 1609 7.00 C 5848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 895 " distance=2.02 Simple disulfide: pdb=" SG CYS A1104 " - pdb=" SG CYS A1139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 3.6 seconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 16 sheets defined 33.7% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 removed outlier: 3.942A pdb=" N ALA A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.501A pdb=" N ILE A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.602A pdb=" N PHE A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 92 through 117 removed outlier: 3.523A pdb=" N GLY A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 112 " --> pdb=" O TRP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.537A pdb=" N ILE A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.820A pdb=" N THR A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.583A pdb=" N LEU A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 166 removed outlier: 3.798A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.740A pdb=" N SER A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 199 through 207 removed outlier: 3.595A pdb=" N TRP A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.946A pdb=" N TRP A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 232 through 243 removed outlier: 4.072A pdb=" N LYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.896A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 removed outlier: 3.634A pdb=" N VAL A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 378 removed outlier: 3.739A pdb=" N ILE A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.672A pdb=" N LEU A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.750A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.873A pdb=" N TRP A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 424' Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.682A pdb=" N ASN A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 503 removed outlier: 3.534A pdb=" N ALA A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.646A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.639A pdb=" N THR A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.547A pdb=" N AHIS A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 621 through 632 removed outlier: 3.574A pdb=" N ARG A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.699A pdb=" N ALA A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 732 removed outlier: 3.506A pdb=" N THR A 731 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 728 through 732' Processing helix chain 'A' and resid 934 through 940 removed outlier: 4.217A pdb=" N LEU A 938 " --> pdb=" O GLN A 934 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 940 " --> pdb=" O ARG A 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 934 through 940' Processing helix chain 'A' and resid 959 through 964 removed outlier: 3.649A pdb=" N ALA A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1096 removed outlier: 3.543A pdb=" N ASN A1095 " --> pdb=" O ASP A1091 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A1096 " --> pdb=" O ASN A1092 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1091 through 1096' Processing helix chain 'A' and resid 1125 through 1130 removed outlier: 3.741A pdb=" N ASP A1130 " --> pdb=" O ARG A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1264 removed outlier: 3.712A pdb=" N GLY A1261 " --> pdb=" O TRP A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1278 Processing helix chain 'A' and resid 1296 through 1307 removed outlier: 3.513A pdb=" N VAL A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A1301 " --> pdb=" O ALA A1297 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A1303 " --> pdb=" O GLY A1299 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1356 removed outlier: 3.684A pdb=" N TYR A1341 " --> pdb=" O ALA A1337 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1349 " --> pdb=" O GLY A1345 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A1354 " --> pdb=" O ALA A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1385 removed outlier: 3.894A pdb=" N GLN A1373 " --> pdb=" O SER A1369 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A1374 " --> pdb=" O TRP A1370 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A1383 " --> pdb=" O SER A1379 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 459 removed outlier: 6.697A pdb=" N ARG A 455 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU A 530 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 457 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL A 532 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 459 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 528 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 595 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY A 566 " --> pdb=" O PRO A 588 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 590 " --> pdb=" O GLN A 564 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN A 564 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 592 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 579 removed outlier: 7.041A pdb=" N VAL A 578 " --> pdb=" O ARG A1061 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1181 through 1182 removed outlier: 3.506A pdb=" N GLN A1236 " --> pdb=" O VAL A1208 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR A1227 " --> pdb=" O VAL A1239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 642 removed outlier: 7.578A pdb=" N ARG A 614 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N THR A 659 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 873 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL A1163 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG A 928 " --> pdb=" O VAL A1163 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A1169 " --> pdb=" O THR A 922 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AA7, first strand: chain 'A' and resid 710 through 714 removed outlier: 6.835A pdb=" N THR A 817 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 794 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 746 removed outlier: 6.797A pdb=" N THR A 774 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 840 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR A 772 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU A 842 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 770 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 745 through 746 removed outlier: 4.678A pdb=" N LEU A 842 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 860 through 862 removed outlier: 4.253A pdb=" N ALA A 860 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 914 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 860 through 862 removed outlier: 4.253A pdb=" N ALA A 860 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 914 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 886 through 887 Processing sheet with id=AB4, first strand: chain 'A' and resid 946 through 948 Processing sheet with id=AB5, first strand: chain 'A' and resid 1036 through 1037 removed outlier: 3.597A pdb=" N LEU A1002 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A1078 " --> pdb=" O ARG A1001 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1027 through 1028 removed outlier: 3.773A pdb=" N ARG A1027 " --> pdb=" O VAL A1016 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP A1054 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1185 through 1186 removed outlier: 3.522A pdb=" N ARG A1219 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A1251 " --> pdb=" O ALA A1217 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 876 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: 3.99 Time building geometry restraints manager: 3.68 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: 2824 1.33 - 1.45: 1376 1.45 - 1.57: 5147 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 9377 Sorted by residual: bond pdb=" CB VAL A1229 " pdb=" CG2 VAL A1229 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.10e+00 bond pdb=" CG LEU A 559 " pdb=" CD2 LEU A 559 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.62e+00 bond pdb=" CB VAL A1239 " pdb=" CG2 VAL A1239 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.93e+00 bond pdb=" C VAL A1009 " pdb=" N PRO A1010 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.39e+00 bond pdb=" C ILE A 34 " pdb=" N SER A 35 " ideal model delta sigma weight residual 1.329 1.295 0.034 1.86e-02 2.89e+03 3.29e+00 ... (remaining 9372 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.89: 495 106.89 - 114.54: 5541 114.54 - 122.19: 5125 122.19 - 129.84: 1631 129.84 - 137.49: 100 Bond angle restraints: 12892 Sorted by residual: angle pdb=" C ASP A 37 " pdb=" N THR A 38 " pdb=" CA THR A 38 " ideal model delta sigma weight residual 121.54 132.02 -10.48 1.91e+00 2.74e-01 3.01e+01 angle pdb=" N THR A 661 " pdb=" CA THR A 661 " pdb=" C THR A 661 " ideal model delta sigma weight residual 109.81 120.36 -10.55 2.21e+00 2.05e-01 2.28e+01 angle pdb=" C VAL A1117 " pdb=" CA VAL A1117 " pdb=" CB VAL A1117 " ideal model delta sigma weight residual 111.08 115.07 -3.99 9.50e-01 1.11e+00 1.77e+01 angle pdb=" CA PRO A1010 " pdb=" N PRO A1010 " pdb=" CD PRO A1010 " ideal model delta sigma weight residual 112.00 106.79 5.21 1.40e+00 5.10e-01 1.39e+01 angle pdb=" CA VAL A1009 " pdb=" C VAL A1009 " pdb=" N PRO A1010 " ideal model delta sigma weight residual 118.88 124.45 -5.57 1.54e+00 4.22e-01 1.31e+01 ... (remaining 12887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5111 17.82 - 35.64: 377 35.64 - 53.47: 51 53.47 - 71.29: 4 71.29 - 89.11: 5 Dihedral angle restraints: 5548 sinusoidal: 2007 harmonic: 3541 Sorted by residual: dihedral pdb=" CA GLU A1008 " pdb=" C GLU A1008 " pdb=" N VAL A1009 " pdb=" CA VAL A1009 " ideal model delta harmonic sigma weight residual -180.00 -151.26 -28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PRO A 866 " pdb=" C PRO A 866 " pdb=" N ALA A 867 " pdb=" CA ALA A 867 " ideal model delta harmonic sigma weight residual -180.00 -152.12 -27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO A1010 " pdb=" C PRO A1010 " pdb=" N ALA A1011 " pdb=" CA ALA A1011 " ideal model delta harmonic sigma weight residual 180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 5545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1451 0.118 - 0.235: 89 0.235 - 0.353: 5 0.353 - 0.470: 0 0.470 - 0.588: 1 Chirality restraints: 1546 Sorted by residual: chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.64e+00 chirality pdb=" CA THR A 661 " pdb=" N THR A 661 " pdb=" C THR A 661 " pdb=" CB THR A 661 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB ILE A 491 " pdb=" CA ILE A 491 " pdb=" CG1 ILE A 491 " pdb=" CG2 ILE A 491 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1543 not shown) Planarity restraints: 1661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 155 " -0.048 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO A 156 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 974 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO A 975 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 37 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C ASP A 37 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP A 37 " -0.019 2.00e-02 2.50e+03 pdb=" N THR A 38 " -0.016 2.00e-02 2.50e+03 ... (remaining 1658 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 94 2.61 - 3.19: 7338 3.19 - 3.76: 13386 3.76 - 4.33: 18552 4.33 - 4.90: 32385 Nonbonded interactions: 71755 Sorted by model distance: nonbonded pdb=" O THR A 838 " pdb=" OE2 GLU A 839 " model vdw 2.042 3.040 nonbonded pdb=" O ALA A 962 " pdb="CA CA A2002 " model vdw 2.067 2.510 nonbonded pdb=" OG SER A 715 " pdb=" OE1 GLN A 756 " model vdw 2.243 2.440 nonbonded pdb=" O ASP A 967 " pdb="CA CA A2002 " model vdw 2.263 2.510 nonbonded pdb=" O THR A 970 " pdb="CA CA A2002 " model vdw 2.296 2.510 ... (remaining 71750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 35.270 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.010 0.100 9377 Z= 0.671 Angle : 1.037 12.493 12892 Z= 0.579 Chirality : 0.063 0.588 1546 Planarity : 0.009 0.071 1661 Dihedral : 12.683 89.109 3252 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer: Outliers : 0.32 % Allowed : 6.13 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -5.12 (0.18), residues: 1225 helix: -4.98 (0.08), residues: 382 sheet: -2.14 (0.32), residues: 197 loop : -2.77 (0.20), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 221 HIS 0.014 0.002 HIS A 675 PHE 0.025 0.003 PHE A 433 TYR 0.014 0.002 TYR A1258 ARG 0.005 0.001 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 88 average time/residue: 0.2813 time to fit residues: 33.2249 Evaluate side-chains 63 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0858 time to fit residues: 1.6721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS A1151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9377 Z= 0.218 Angle : 0.623 8.674 12892 Z= 0.311 Chirality : 0.045 0.411 1546 Planarity : 0.006 0.057 1661 Dihedral : 5.175 23.602 1320 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.75 % Allowed : 9.35 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -3.55 (0.20), residues: 1225 helix: -3.10 (0.20), residues: 375 sheet: -1.55 (0.34), residues: 197 loop : -2.12 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 214 HIS 0.003 0.001 HIS A 852 PHE 0.015 0.001 PHE A 246 TYR 0.012 0.002 TYR A 439 ARG 0.003 0.000 ARG A1061 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.084 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 80 average time/residue: 0.2103 time to fit residues: 25.0407 Evaluate side-chains 71 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0987 time to fit residues: 2.9810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 112 optimal weight: 0.0980 chunk 38 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9377 Z= 0.182 Angle : 0.577 8.414 12892 Z= 0.279 Chirality : 0.044 0.440 1546 Planarity : 0.005 0.051 1661 Dihedral : 4.489 19.062 1320 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.65 % Allowed : 10.22 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.22), residues: 1225 helix: -1.70 (0.25), residues: 374 sheet: -1.12 (0.35), residues: 197 loop : -1.71 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 972 HIS 0.002 0.001 HIS A 675 PHE 0.023 0.001 PHE A 246 TYR 0.009 0.001 TYR A 439 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 1.039 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 77 average time/residue: 0.1911 time to fit residues: 22.3697 Evaluate side-chains 63 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1020 time to fit residues: 1.9069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 0.0010 chunk 108 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 65 GLN A 626 ASN A1151 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9377 Z= 0.262 Angle : 0.594 8.609 12892 Z= 0.288 Chirality : 0.046 0.511 1546 Planarity : 0.005 0.051 1661 Dihedral : 4.512 19.090 1320 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.18 % Allowed : 10.75 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.23), residues: 1225 helix: -1.19 (0.26), residues: 383 sheet: -0.94 (0.36), residues: 197 loop : -1.57 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.004 0.001 HIS A 675 PHE 0.013 0.001 PHE A 246 TYR 0.013 0.001 TYR A 439 ARG 0.005 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 1.291 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 67 average time/residue: 0.2638 time to fit residues: 26.2295 Evaluate side-chains 70 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0925 time to fit residues: 3.3812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 0.0060 chunk 49 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 chunk 108 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9377 Z= 0.163 Angle : 0.547 8.286 12892 Z= 0.263 Chirality : 0.044 0.522 1546 Planarity : 0.004 0.047 1661 Dihedral : 4.196 17.523 1320 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.11 % Allowed : 11.94 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -1.56 (0.24), residues: 1225 helix: -0.52 (0.28), residues: 375 sheet: -0.75 (0.36), residues: 198 loop : -1.42 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.002 0.000 HIS A 551 PHE 0.007 0.001 PHE A 433 TYR 0.009 0.001 TYR A 439 ARG 0.005 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.959 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.2380 time to fit residues: 24.2427 Evaluate side-chains 64 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1023 time to fit residues: 1.6124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9377 Z= 0.246 Angle : 0.576 8.503 12892 Z= 0.278 Chirality : 0.046 0.555 1546 Planarity : 0.005 0.048 1661 Dihedral : 4.267 18.182 1320 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.65 % Allowed : 12.26 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -1.37 (0.24), residues: 1225 helix: -0.29 (0.28), residues: 376 sheet: -0.67 (0.36), residues: 198 loop : -1.34 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.004 0.001 HIS A 675 PHE 0.011 0.001 PHE A 433 TYR 0.012 0.001 TYR A 439 ARG 0.004 0.000 ARG A 764 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.967 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.2551 time to fit residues: 21.8181 Evaluate side-chains 60 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0928 time to fit residues: 2.1614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 120 optimal weight: 0.0570 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 0.0030 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9377 Z= 0.159 Angle : 0.536 8.243 12892 Z= 0.257 Chirality : 0.044 0.560 1546 Planarity : 0.004 0.044 1661 Dihedral : 4.039 16.639 1320 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.65 % Allowed : 12.47 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -1.10 (0.24), residues: 1225 helix: 0.04 (0.28), residues: 370 sheet: -0.51 (0.37), residues: 198 loop : -1.23 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.002 0.000 HIS A 551 PHE 0.007 0.001 PHE A 75 TYR 0.009 0.001 TYR A 439 ARG 0.003 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.026 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 0.2607 time to fit residues: 25.4632 Evaluate side-chains 68 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0888 time to fit residues: 1.8456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.0050 chunk 76 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 0.0970 chunk 109 optimal weight: 0.6980 chunk 115 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A1232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9377 Z= 0.145 Angle : 0.525 8.185 12892 Z= 0.251 Chirality : 0.044 0.584 1546 Planarity : 0.004 0.043 1661 Dihedral : 3.868 16.183 1320 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.54 % Allowed : 13.76 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -0.83 (0.24), residues: 1225 helix: 0.31 (0.28), residues: 382 sheet: -0.32 (0.38), residues: 197 loop : -1.14 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.001 0.000 HIS A 551 PHE 0.010 0.001 PHE A1066 TYR 0.009 0.001 TYR A 439 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.978 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.2372 time to fit residues: 23.3915 Evaluate side-chains 66 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2232 time to fit residues: 2.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9377 Z= 0.193 Angle : 0.550 8.344 12892 Z= 0.262 Chirality : 0.045 0.592 1546 Planarity : 0.004 0.043 1661 Dihedral : 3.925 16.382 1320 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.22 % Allowed : 13.87 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1225 helix: 0.59 (0.28), residues: 370 sheet: -0.29 (0.38), residues: 197 loop : -1.08 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.003 0.001 HIS A 675 PHE 0.008 0.001 PHE A 433 TYR 0.011 0.001 TYR A 439 ARG 0.006 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.900 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.2291 time to fit residues: 21.3001 Evaluate side-chains 64 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0876 time to fit residues: 1.5689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.0040 chunk 82 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9377 Z= 0.164 Angle : 0.535 8.241 12892 Z= 0.255 Chirality : 0.045 0.597 1546 Planarity : 0.004 0.043 1661 Dihedral : 3.861 16.406 1320 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.22 % Allowed : 13.98 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -0.56 (0.25), residues: 1225 helix: 0.70 (0.28), residues: 377 sheet: -0.23 (0.38), residues: 197 loop : -1.05 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.002 0.000 HIS A 675 PHE 0.009 0.001 PHE A1066 TYR 0.010 0.001 TYR A 439 ARG 0.005 0.000 ARG A 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 1.067 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 0.2210 time to fit residues: 21.7733 Evaluate side-chains 64 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1206 time to fit residues: 1.5670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.149209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124913 restraints weight = 35005.926| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.20 r_work: 0.3297 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9377 Z= 0.213 Angle : 0.559 8.374 12892 Z= 0.267 Chirality : 0.045 0.595 1546 Planarity : 0.004 0.045 1661 Dihedral : 3.956 16.634 1320 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 14.30 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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 (0.25), residues: 1225 helix: 0.80 (0.28), residues: 370 sheet: -0.26 (0.38), residues: 198 loop : -1.02 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.003 0.001 HIS A 675 PHE 0.009 0.001 PHE A 433 TYR 0.011 0.001 TYR A 439 ARG 0.006 0.000 ARG A 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.51 seconds wall clock time: 35 minutes 45.22 seconds (2145.22 seconds total)