Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 23:55:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kiy_22890/10_2023/7kiy_22890.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kiy_22890/10_2023/7kiy_22890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kiy_22890/10_2023/7kiy_22890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kiy_22890/10_2023/7kiy_22890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kiy_22890/10_2023/7kiy_22890.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kiy_22890/10_2023/7kiy_22890.pdb" } resolution = 2.92 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 98 5.16 5 C 12931 2.51 5 N 3169 2.21 5 O 3672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 634": "OD1" <-> "OD2" Residue "A TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A ASP 751": "OD1" <-> "OD2" Residue "A ASP 754": "OD1" <-> "OD2" Residue "A PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A ASP 782": "OD1" <-> "OD2" Residue "A TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 814": "OD1" <-> "OD2" Residue "A PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A ASP 924": "OD1" <-> "OD2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "A PHE 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1054": "OD1" <-> "OD2" Residue "A TYR 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1243": "OD1" <-> "OD2" Residue "A TYR 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1309": "OD1" <-> "OD2" Residue "A ASP 1333": "OD1" <-> "OD2" Residue "A ASP 1339": "OD1" <-> "OD2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 433": "NH1" <-> "NH2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "B ASP 513": "OD1" <-> "OD2" Residue "B PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 783": "OD1" <-> "OD2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "B ASP 838": "OD1" <-> "OD2" Residue "B ASP 840": "OD1" <-> "OD2" Residue "B PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 885": "OD1" <-> "OD2" Residue "B ASP 888": "OD1" <-> "OD2" Residue "B GLU 900": "OE1" <-> "OE2" Residue "B TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 302": "OD1" <-> "OD2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C ASP 353": "OD1" <-> "OD2" Residue "C TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 409": "OD1" <-> "OD2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 579": "OE1" <-> "OE2" Residue "C GLU 595": "OE1" <-> "OE2" Residue "C PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 647": "OD1" <-> "OD2" Residue "C GLU 666": "OE1" <-> "OE2" Residue "C ASP 669": "OD1" <-> "OD2" Residue "C PHE 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 19870 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9817 Classifications: {'peptide': 1169} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 25, 'TRANS': 1139} Chain breaks: 3 Chain: "B" Number of atoms: 4308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4308 Classifications: {'peptide': 516} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 506} Chain breaks: 5 Chain: "C" Number of atoms: 5745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5745 Classifications: {'peptide': 691} Link IDs: {'CIS': 3, 'PTRANS': 28, 'TRANS': 659} Time building chain proxies: 10.63, per 1000 atoms: 0.53 Number of scatterers: 19870 At special positions: 0 Unit cell: (162.12, 114.24, 156.24, 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 98 16.00 O 3672 8.00 N 3169 7.00 C 12931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 363 " distance=1.59 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 519 " - pdb=" SG CYS A 547 " distance=2.30 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 544 " distance=2.04 Simple disulfide: pdb=" SG CYS A1352 " - pdb=" SG CYS A1355 " distance=2.03 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 240 " distance=2.02 Simple disulfide: pdb=" SG CYS B 791 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 244 " - pdb=" SG CYS C 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS C 276 " distance=2.32 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 536 " distance=2.21 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: 7.61 Conformation dependent library (CDL) restraints added in 2.7 seconds 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4636 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 3 sheets defined 58.8% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.778A pdb=" N SER A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 87 removed outlier: 3.515A pdb=" N LYS A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.593A pdb=" N LYS A 107 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 147 Processing helix chain 'A' and resid 154 through 181 removed outlier: 3.832A pdb=" N LYS A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 4.196A pdb=" N GLN A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 removed outlier: 3.678A pdb=" N PHE A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.841A pdb=" N PHE A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.656A pdb=" N THR A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 238' Processing helix chain 'A' and resid 260 through 274 removed outlier: 3.832A pdb=" N MET A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.800A pdb=" N HIS A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 301 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.587A pdb=" N LEU A 320 " --> pdb=" O TRP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 removed outlier: 4.075A pdb=" N LYS A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 361 through 385 removed outlier: 3.935A pdb=" N GLN A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 removed outlier: 3.562A pdb=" N PHE A 407 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.596A pdb=" N THR A 420 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 459 removed outlier: 3.522A pdb=" N ASN A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 464 through 480 removed outlier: 3.794A pdb=" N ASN A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 490 through 491 No H-bonds generated for 'chain 'A' and resid 490 through 491' Processing helix chain 'A' and resid 492 through 503 removed outlier: 3.608A pdb=" N TYR A 495 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN A 497 " --> pdb=" O GLY A 494 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ALA A 498 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 499 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 500 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 503 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 removed outlier: 3.613A pdb=" N LEU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 542 through 555 removed outlier: 3.580A pdb=" N LEU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 removed outlier: 3.523A pdb=" N LYS A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 599 removed outlier: 3.557A pdb=" N SER A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 614 removed outlier: 3.805A pdb=" N THR A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.814A pdb=" N ILE A 619 " --> pdb=" O PHE A 616 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER A 620 " --> pdb=" O LYS A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.851A pdb=" N ILE A 632 " --> pdb=" O MET A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 675 Processing helix chain 'A' and resid 680 through 686 Processing helix chain 'A' and resid 693 through 699 removed outlier: 3.795A pdb=" N GLN A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 732 Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 758 removed outlier: 4.378A pdb=" N ASP A 751 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 758 " --> pdb=" O ASP A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 786 removed outlier: 3.716A pdb=" N TRP A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 772 " --> pdb=" O GLN A 768 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 removed outlier: 3.978A pdb=" N LEU A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 819 Processing helix chain 'A' and resid 877 through 893 removed outlier: 4.022A pdb=" N GLU A 881 " --> pdb=" O GLU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 916 removed outlier: 3.745A pdb=" N GLN A 904 " --> pdb=" O THR A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 961 removed outlier: 3.868A pdb=" N ILE A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 952 " --> pdb=" O ARG A 948 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG A 959 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 977 removed outlier: 3.883A pdb=" N ALA A 967 " --> pdb=" O LYS A 963 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 968 " --> pdb=" O THR A 964 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 975 " --> pdb=" O MET A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 987 Processing helix chain 'A' and resid 998 through 1022 removed outlier: 3.902A pdb=" N ILE A1014 " --> pdb=" O TYR A1010 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A1022 " --> pdb=" O VAL A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1033 removed outlier: 3.728A pdb=" N GLN A1033 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1056 removed outlier: 3.837A pdb=" N ASN A1044 " --> pdb=" O PHE A1040 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A1056 " --> pdb=" O MET A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1071 removed outlier: 4.004A pdb=" N LEU A1064 " --> pdb=" O ASN A1060 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1164 Processing helix chain 'A' and resid 1202 through 1224 removed outlier: 3.596A pdb=" N CYS A1217 " --> pdb=" O MET A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1235 removed outlier: 3.659A pdb=" N ILE A1235 " --> pdb=" O ASN A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1260 removed outlier: 4.196A pdb=" N ARG A1244 " --> pdb=" O ARG A1240 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1294 removed outlier: 3.891A pdb=" N LYS A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1322 removed outlier: 4.074A pdb=" N ASN A1314 " --> pdb=" O ASP A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1325 No H-bonds generated for 'chain 'A' and resid 1323 through 1325' Processing helix chain 'A' and resid 1345 through 1350 Processing helix chain 'B' and resid 236 through 260 removed outlier: 3.872A pdb=" N GLU B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 removed outlier: 3.943A pdb=" N LEU B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 265' Processing helix chain 'B' and resid 274 through 280 removed outlier: 3.942A pdb=" N LYS B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 376 removed outlier: 4.257A pdb=" N SER B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 388 removed outlier: 4.155A pdb=" N PHE B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 405 removed outlier: 3.686A pdb=" N ASN B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 494 through 504 removed outlier: 4.062A pdb=" N TYR B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 528 removed outlier: 3.826A pdb=" N LEU B 520 " --> pdb=" O ASP B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 568 through 569 No H-bonds generated for 'chain 'B' and resid 568 through 569' Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 573 through 588 removed outlier: 3.667A pdb=" N HIS B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 587 " --> pdb=" O ASN B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 609 removed outlier: 3.721A pdb=" N THR B 593 " --> pdb=" O ASN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 658 removed outlier: 3.688A pdb=" N ILE B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.625A pdb=" N LEU B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 688 " --> pdb=" O ILE B 684 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 739 through 755 removed outlier: 3.693A pdb=" N SER B 743 " --> pdb=" O PHE B 739 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 744 " --> pdb=" O VAL B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 798 Processing helix chain 'B' and resid 810 through 829 removed outlier: 3.877A pdb=" N ALA B 828 " --> pdb=" O VAL B 824 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 829 " --> pdb=" O THR B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 854 removed outlier: 3.568A pdb=" N LEU B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 870 removed outlier: 4.053A pdb=" N LEU B 863 " --> pdb=" O ILE B 859 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 870 " --> pdb=" O ASN B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 895 removed outlier: 3.526A pdb=" N LYS B 884 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS B 895 " --> pdb=" O LEU B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 915 Processing helix chain 'C' and resid 33 through 49 removed outlier: 3.517A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 38 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 77 removed outlier: 3.793A pdb=" N PHE C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 71 " --> pdb=" O PRO C 67 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.659A pdb=" N LYS C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 135 removed outlier: 4.259A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.526A pdb=" N LYS C 186 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 187 " --> pdb=" O GLU C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'C' and resid 195 through 203 removed outlier: 3.506A pdb=" N TYR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.557A pdb=" N GLU C 243 " --> pdb=" O HIS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.586A pdb=" N LEU C 282 " --> pdb=" O HIS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 298 Processing helix chain 'C' and resid 371 through 377 Processing helix chain 'C' and resid 379 through 382 removed outlier: 3.662A pdb=" N TYR C 382 " --> pdb=" O ASP C 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 379 through 382' Processing helix chain 'C' and resid 383 through 392 removed outlier: 3.534A pdb=" N LYS C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 420 through 424 removed outlier: 4.278A pdb=" N ASN C 423 " --> pdb=" O GLN C 420 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 424 " --> pdb=" O CYS C 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 420 through 424' Processing helix chain 'C' and resid 433 through 454 removed outlier: 3.861A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.718A pdb=" N HIS C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 482 " --> pdb=" O ILE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 514 removed outlier: 4.296A pdb=" N TYR C 507 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 514 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 518 removed outlier: 3.971A pdb=" N LEU C 518 " --> pdb=" O VAL C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 515 through 518' Processing helix chain 'C' and resid 529 through 536 Processing helix chain 'C' and resid 542 through 548 removed outlier: 4.012A pdb=" N VAL C 546 " --> pdb=" O HIS C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 570 Processing helix chain 'C' and resid 577 through 591 removed outlier: 3.899A pdb=" N TYR C 589 " --> pdb=" O PHE C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 620 removed outlier: 3.667A pdb=" N LEU C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 616 " --> pdb=" O GLU C 612 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS C 620 " --> pdb=" O GLU C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 630 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 635 through 651 removed outlier: 3.773A pdb=" N ASP C 640 " --> pdb=" O PRO C 636 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 641 " --> pdb=" O ASN C 637 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 651 " --> pdb=" O ASP C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 666 Processing helix chain 'C' and resid 672 through 690 removed outlier: 3.510A pdb=" N THR C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA C 679 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 680 " --> pdb=" O VAL C 676 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 112 Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 692 removed outlier: 6.620A pdb=" N GLY A 871 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 148 through 150 834 hydrogen bonds defined for protein. 2454 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: 5.29 Time building geometry restraints manager: 8.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.25: 3208 1.25 - 1.41: 5435 1.41 - 1.56: 11535 1.56 - 1.72: 4 1.72 - 1.88: 158 Bond restraints: 20340 Sorted by residual: bond pdb=" C SER C 479 " pdb=" O SER C 479 " ideal model delta sigma weight residual 1.237 1.095 0.142 1.31e-02 5.83e+03 1.17e+02 bond pdb=" C ILE C 476 " pdb=" O ILE C 476 " ideal model delta sigma weight residual 1.237 1.121 0.116 1.13e-02 7.83e+03 1.06e+02 bond pdb=" C LEU C 477 " pdb=" O LEU C 477 " ideal model delta sigma weight residual 1.236 1.111 0.125 1.29e-02 6.01e+03 9.38e+01 bond pdb=" C CYS A 547 " pdb=" O CYS A 547 " ideal model delta sigma weight residual 1.237 1.124 0.112 1.16e-02 7.43e+03 9.38e+01 bond pdb=" CA SER C 479 " pdb=" CB SER C 479 " ideal model delta sigma weight residual 1.531 1.382 0.149 1.56e-02 4.11e+03 9.14e+01 ... (remaining 20335 not shown) Histogram of bond angle deviations from ideal: 86.60 - 96.11: 3 96.11 - 105.61: 297 105.61 - 115.11: 12042 115.11 - 124.61: 14827 124.61 - 134.12: 252 Bond angle restraints: 27421 Sorted by residual: angle pdb=" N ILE A 520 " pdb=" CA ILE A 520 " pdb=" C ILE A 520 " ideal model delta sigma weight residual 111.45 100.08 11.37 9.30e-01 1.16e+00 1.49e+02 angle pdb=" CA CYS C 536 " pdb=" CB CYS C 536 " pdb=" SG CYS C 536 " ideal model delta sigma weight residual 114.40 86.60 27.80 2.30e+00 1.89e-01 1.46e+02 angle pdb=" C ILE A 520 " pdb=" CA ILE A 520 " pdb=" CB ILE A 520 " ideal model delta sigma weight residual 111.92 97.77 14.15 1.31e+00 5.83e-01 1.17e+02 angle pdb=" C CYS C 475 " pdb=" CA CYS C 475 " pdb=" CB CYS C 475 " ideal model delta sigma weight residual 110.88 94.38 16.50 1.57e+00 4.06e-01 1.10e+02 angle pdb=" N CYS C 536 " pdb=" CA CYS C 536 " pdb=" C CYS C 536 " ideal model delta sigma weight residual 112.87 125.06 -12.19 1.20e+00 6.94e-01 1.03e+02 ... (remaining 27416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 10982 18.16 - 36.32: 1060 36.32 - 54.48: 178 54.48 - 72.65: 27 72.65 - 90.81: 13 Dihedral angle restraints: 12260 sinusoidal: 5089 harmonic: 7171 Sorted by residual: dihedral pdb=" CA TYR B 876 " pdb=" C TYR B 876 " pdb=" N GLY B 877 " pdb=" CA GLY B 877 " ideal model delta harmonic sigma weight residual -180.00 -89.19 -90.81 0 5.00e+00 4.00e-02 3.30e+02 dihedral pdb=" CA TYR A 92 " pdb=" C TYR A 92 " pdb=" N PRO A 93 " pdb=" CA PRO A 93 " ideal model delta harmonic sigma weight residual -180.00 -112.77 -67.23 0 5.00e+00 4.00e-02 1.81e+02 dihedral pdb=" CA GLN B 535 " pdb=" C GLN B 535 " pdb=" N ASN B 536 " pdb=" CA ASN B 536 " ideal model delta harmonic sigma weight residual -180.00 -139.58 -40.42 0 5.00e+00 4.00e-02 6.54e+01 ... (remaining 12257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2953 0.173 - 0.346: 14 0.346 - 0.520: 5 0.520 - 0.693: 0 0.693 - 0.866: 1 Chirality restraints: 2973 Sorted by residual: chirality pdb=" CA CYS A 363 " pdb=" N CYS A 363 " pdb=" C CYS A 363 " pdb=" CB CYS A 363 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CA SER B 880 " pdb=" N SER B 880 " pdb=" C SER B 880 " pdb=" CB SER B 880 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" CA GLN A 518 " pdb=" N GLN A 518 " pdb=" C GLN A 518 " pdb=" CB GLN A 518 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 2970 not shown) Planarity restraints: 3444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 870 " 0.028 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C SER B 870 " -0.104 2.00e-02 2.50e+03 pdb=" O SER B 870 " 0.042 2.00e-02 2.50e+03 pdb=" N CYS B 871 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 92 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 93 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 479 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C SER C 479 " -0.066 2.00e-02 2.50e+03 pdb=" O SER C 479 " 0.025 2.00e-02 2.50e+03 pdb=" N THR C 480 " 0.022 2.00e-02 2.50e+03 ... (remaining 3441 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 7 2.07 - 2.78: 4673 2.78 - 3.49: 26298 3.49 - 4.19: 42656 4.19 - 4.90: 78547 Nonbonded interactions: 152181 Sorted by model distance: nonbonded pdb=" O LYS B 879 " pdb=" CD1 LEU B 883 " model vdw 1.366 3.460 nonbonded pdb=" O ALA C 539 " pdb=" N LEU C 541 " model vdw 1.716 2.520 nonbonded pdb=" O ILE B 878 " pdb=" CD2 LEU B 883 " model vdw 1.719 3.460 nonbonded pdb=" CG2 ILE B 878 " pdb=" CG LEU B 883 " model vdw 1.817 3.890 nonbonded pdb=" CG2 ILE B 878 " pdb=" CD2 LEU B 883 " model vdw 1.960 3.880 ... (remaining 152176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 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: 0.030 Extract box with map and model: 15.040 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 49.500 Find NCS groups from input model: 0.490 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:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.008 0.154 20340 Z= 0.489 Angle : 0.929 27.797 27421 Z= 0.538 Chirality : 0.054 0.866 2973 Planarity : 0.005 0.102 3444 Dihedral : 14.296 90.807 7591 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.68 % Favored : 83.56 % Rotamer: Outliers : 0.85 % Allowed : 4.69 % Favored : 94.46 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.30 % Twisted Proline : 3.28 % Twisted General : 0.39 % 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: -4.17 (0.14), residues: 2354 helix: -1.55 (0.13), residues: 1282 sheet: -3.44 (0.61), residues: 54 loop : -4.46 (0.14), residues: 1018 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 290 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 308 average time/residue: 1.2597 time to fit residues: 439.4334 Evaluate side-chains 157 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.3812 time to fit residues: 3.8130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 137 optimal weight: 8.9990 chunk 214 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 392 HIS A 422 GLN A 474 ASN A 600 HIS A 693 HIS A 759 GLN A 797 HIS A1044 ASN A1057 ASN A1255 ASN B 407 ASN B 430 ASN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 GLN B 536 ASN B 700 ASN B 755 HIS C 76 HIS C 166 ASN C 181 ASN C 330 GLN C 361 ASN C 481 HIS C 527 ASN C 542 HIS C 635 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 20340 Z= 0.185 Angle : 0.709 13.347 27421 Z= 0.368 Chirality : 0.042 0.198 2973 Planarity : 0.004 0.090 3444 Dihedral : 6.358 62.254 2600 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.25 % Favored : 84.58 % Rotamer: Outliers : 2.73 % Allowed : 11.75 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.30 % Twisted Proline : 3.28 % Twisted General : 0.13 % 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: -2.77 (0.16), residues: 2354 helix: -0.24 (0.14), residues: 1296 sheet: -2.59 (0.93), residues: 29 loop : -4.12 (0.15), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 190 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 22 residues processed: 234 average time/residue: 1.1516 time to fit residues: 312.0220 Evaluate side-chains 162 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 15 residues processed: 8 average time/residue: 0.4696 time to fit residues: 8.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 0.3980 chunk 212 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN A 285 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 ASN A1346 GLN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 781 HIS C 154 HIS C 468 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20340 Z= 0.323 Angle : 0.745 13.973 27421 Z= 0.390 Chirality : 0.045 0.183 2973 Planarity : 0.005 0.099 3444 Dihedral : 6.334 64.963 2600 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.93 % Favored : 83.94 % Rotamer: Outliers : 3.04 % Allowed : 14.30 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.30 % Twisted Proline : 3.28 % Twisted General : 0.22 % 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: -2.19 (0.17), residues: 2354 helix: 0.28 (0.15), residues: 1299 sheet: -2.80 (0.85), residues: 40 loop : -3.93 (0.16), residues: 1015 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 158 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 32 residues processed: 206 average time/residue: 1.1006 time to fit residues: 264.2533 Evaluate side-chains 171 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 9 average time/residue: 0.5902 time to fit residues: 10.0735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS A1057 ASN B 515 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20340 Z= 0.190 Angle : 0.674 13.597 27421 Z= 0.347 Chirality : 0.042 0.186 2973 Planarity : 0.004 0.091 3444 Dihedral : 5.940 61.072 2600 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.70 % Favored : 85.13 % Rotamer: Outliers : 2.68 % Allowed : 16.09 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.30 % Twisted Proline : 3.28 % Twisted General : 0.09 % 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: -1.69 (0.17), residues: 2354 helix: 0.73 (0.15), residues: 1294 sheet: -2.05 (0.98), residues: 24 loop : -3.77 (0.16), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 165 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 27 residues processed: 209 average time/residue: 0.9935 time to fit residues: 245.7545 Evaluate side-chains 172 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 8 average time/residue: 0.3965 time to fit residues: 7.4360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 194 optimal weight: 0.2980 chunk 157 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20340 Z= 0.248 Angle : 0.698 14.174 27421 Z= 0.359 Chirality : 0.043 0.320 2973 Planarity : 0.004 0.107 3444 Dihedral : 5.888 62.714 2600 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.55 % Favored : 84.28 % Rotamer: Outliers : 2.99 % Allowed : 17.78 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.30 % Twisted Proline : 3.28 % Twisted General : 0.09 % 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: -1.60 (0.17), residues: 2354 helix: 0.75 (0.15), residues: 1312 sheet: -1.72 (0.81), residues: 34 loop : -3.74 (0.16), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 155 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 33 residues processed: 204 average time/residue: 1.0063 time to fit residues: 242.7468 Evaluate side-chains 179 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 2.485 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 10 average time/residue: 0.4402 time to fit residues: 9.4910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.5980 chunk 205 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 0.0970 chunk 56 optimal weight: 0.9990 chunk 228 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20340 Z= 0.161 Angle : 0.651 13.211 27421 Z= 0.334 Chirality : 0.041 0.203 2973 Planarity : 0.004 0.096 3444 Dihedral : 5.633 59.575 2600 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.19 % Favored : 85.68 % Rotamer: Outliers : 2.55 % Allowed : 18.32 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.30 % Twisted Proline : 3.28 % Twisted General : 0.09 % 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: -1.30 (0.18), residues: 2354 helix: 1.03 (0.15), residues: 1303 sheet: -1.44 (1.06), residues: 24 loop : -3.59 (0.17), residues: 1027 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 168 time to evaluate : 2.442 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 29 residues processed: 213 average time/residue: 0.9626 time to fit residues: 243.7096 Evaluate side-chains 175 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 2.370 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 6 average time/residue: 0.3162 time to fit residues: 6.1730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 192 optimal weight: 0.0970 chunk 127 optimal weight: 0.3980 chunk 227 optimal weight: 0.0770 chunk 142 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 920 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 20340 Z= 0.159 Angle : 0.661 12.916 27421 Z= 0.336 Chirality : 0.041 0.201 2973 Planarity : 0.004 0.103 3444 Dihedral : 5.466 59.458 2600 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.44 % Favored : 85.47 % Rotamer: Outliers : 2.37 % Allowed : 19.35 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.26 % Twisted Proline : 3.28 % Twisted General : 0.13 % 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: -1.06 (0.18), residues: 2354 helix: 1.28 (0.15), residues: 1287 sheet: -1.21 (1.07), residues: 24 loop : -3.52 (0.17), residues: 1043 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 163 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 203 average time/residue: 1.0179 time to fit residues: 245.2550 Evaluate side-chains 173 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 2.649 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 5 average time/residue: 0.7330 time to fit residues: 7.9950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 206 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20340 Z= 0.207 Angle : 0.684 12.871 27421 Z= 0.349 Chirality : 0.042 0.201 2973 Planarity : 0.004 0.111 3444 Dihedral : 5.464 61.051 2600 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.32 % Favored : 85.51 % Rotamer: Outliers : 2.28 % Allowed : 20.15 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.26 % Twisted Proline : 3.28 % Twisted General : 0.13 % 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: -1.03 (0.18), residues: 2354 helix: 1.26 (0.15), residues: 1296 sheet: -1.30 (1.06), residues: 24 loop : -3.46 (0.17), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 149 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 33 residues processed: 190 average time/residue: 0.9785 time to fit residues: 221.0754 Evaluate side-chains 176 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 28 residues processed: 7 average time/residue: 0.6148 time to fit residues: 8.8084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 6.9990 chunk 198 optimal weight: 0.2980 chunk 211 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 200 optimal weight: 0.4980 chunk 139 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20340 Z= 0.232 Angle : 0.710 13.198 27421 Z= 0.361 Chirality : 0.043 0.202 2973 Planarity : 0.004 0.112 3444 Dihedral : 5.545 63.708 2600 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.21 % Favored : 84.62 % Rotamer: Outliers : 1.83 % Allowed : 20.60 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.26 % Twisted Proline : 3.28 % Twisted General : 0.13 % 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: -1.05 (0.18), residues: 2354 helix: 1.26 (0.15), residues: 1295 sheet: -1.27 (1.08), residues: 24 loop : -3.49 (0.17), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 30 residues processed: 184 average time/residue: 1.0452 time to fit residues: 228.4968 Evaluate side-chains 177 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 2.529 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 5 average time/residue: 0.4218 time to fit residues: 6.3993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 chunk 216 optimal weight: 0.0570 chunk 187 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 148 optimal weight: 0.4980 chunk 199 optimal weight: 3.9990 overall best weight: 1.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20340 Z= 0.264 Angle : 0.731 13.493 27421 Z= 0.373 Chirality : 0.044 0.216 2973 Planarity : 0.004 0.116 3444 Dihedral : 5.651 64.911 2600 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.08 % Favored : 84.75 % Rotamer: Outliers : 1.70 % Allowed : 20.78 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.26 % Twisted Proline : 3.28 % Twisted General : 0.13 % 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: -1.12 (0.18), residues: 2354 helix: 1.16 (0.15), residues: 1303 sheet: -1.23 (1.09), residues: 24 loop : -3.49 (0.17), residues: 1027 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 31 residues processed: 177 average time/residue: 1.0516 time to fit residues: 218.8368 Evaluate side-chains 166 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 7 average time/residue: 0.6341 time to fit residues: 8.8784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 187 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** 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 = 0.3938 r_free = 0.3938 target = 0.112651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.074528 restraints weight = 48426.144| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.26 r_work: 0.3075 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20340 Z= 0.178 Angle : 0.708 13.828 27421 Z= 0.355 Chirality : 0.042 0.207 2973 Planarity : 0.004 0.107 3444 Dihedral : 5.479 60.460 2600 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.32 % Favored : 85.56 % Rotamer: Outliers : 1.43 % Allowed : 21.05 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.26 % Twisted Proline : 3.28 % Twisted General : 0.13 % 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: -0.95 (0.18), residues: 2354 helix: 1.32 (0.15), residues: 1303 sheet: -1.02 (1.13), residues: 24 loop : -3.45 (0.17), residues: 1027 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5976.18 seconds wall clock time: 108 minutes 13.21 seconds (6493.21 seconds total)