Starting phenix.real_space_refine on Mon Dec 11 13:15:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1s_21016/12_2023/6v1s_21016.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1s_21016/12_2023/6v1s_21016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1s_21016/12_2023/6v1s_21016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1s_21016/12_2023/6v1s_21016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1s_21016/12_2023/6v1s_21016.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1s_21016/12_2023/6v1s_21016.pdb" } resolution = 3.8 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= 0.005 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 14 9.91 5 S 26 5.16 5 C 11235 2.51 5 N 2935 2.21 5 O 3754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B GLU 426": "OE1" <-> "OE2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B GLU 552": "OE1" <-> "OE2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D ASP 537": "OD1" <-> "OD2" Residue "D GLU 544": "OE1" <-> "OE2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 290": "NH1" <-> "NH2" Residue "E ASP 417": "OD1" <-> "OD2" Residue "E ASP 437": "OD1" <-> "OD2" Residue "E ARG 458": "NH1" <-> "NH2" Residue "E ASP 520": "OD1" <-> "OD2" Residue "E GLU 522": "OE1" <-> "OE2" Residue "E GLU 524": "OE1" <-> "OE2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ASP 437": "OD1" <-> "OD2" Residue "F ARG 458": "NH1" <-> "NH2" Residue "F GLU 539": "OE1" <-> "OE2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G GLU 288": "OE1" <-> "OE2" Residue "G ARG 290": "NH1" <-> "NH2" Residue "G GLU 426": "OE1" <-> "OE2" Residue "G ARG 458": "NH1" <-> "NH2" Residue "G GLU 499": "OE1" <-> "OE2" Residue "G ASP 520": "OD1" <-> "OD2" Residue "G GLU 522": "OE1" <-> "OE2" Residue "G GLU 524": "OE1" <-> "OE2" Residue "G GLU 527": "OE1" <-> "OE2" Residue "Z ASP 52": "OD1" <-> "OD2" Residue "Z GLU 55": "OE1" <-> "OE2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z ASP 223": "OD1" <-> "OD2" Residue "Z ASP 252": "OD1" <-> "OD2" Residue "Z GLU 387": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17964 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2114 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 1 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2081 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain breaks: 1 Chain: "C" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2058 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain breaks: 1 Chain: "D" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2122 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 1 Chain: "E" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2153 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 12, 'TRANS': 263} Chain breaks: 1 Chain: "F" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2114 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 1 Chain: "G" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2122 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 1 Chain: "Z" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3186 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.48, per 1000 atoms: 0.47 Number of scatterers: 17964 At special positions: 0 Unit cell: (136.73, 123.17, 119.78, 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 14 19.99 S 26 16.00 O 3754 8.00 N 2935 7.00 C 11235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.89 Conformation dependent library (CDL) restraints added in 3.0 seconds 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4278 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 22.4% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.234A pdb=" N GLN A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 253' Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.029A pdb=" N ILE A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 502 through 506 removed outlier: 4.030A pdb=" N ASP A 505 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.823A pdb=" N GLU A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.858A pdb=" N ALA B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 512 removed outlier: 4.467A pdb=" N TYR B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 290 removed outlier: 4.102A pdb=" N ARG C 290 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 473 removed outlier: 3.621A pdb=" N ALA C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 513 removed outlier: 3.759A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 removed outlier: 4.399A pdb=" N GLU C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 272 through 278 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 507 through 513 removed outlier: 3.814A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 removed outlier: 4.099A pdb=" N GLU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.642A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.738A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 473 removed outlier: 3.786A pdb=" N ALA E 472 " --> pdb=" O LYS E 468 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 511 Processing helix chain 'E' and resid 546 through 556 removed outlier: 4.816A pdb=" N GLU E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE E 555 " --> pdb=" O ILE E 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 272 through 279 removed outlier: 3.872A pdb=" N GLY F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 473 removed outlier: 3.616A pdb=" N LEU F 467 " --> pdb=" O ASN F 463 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA F 472 " --> pdb=" O LYS F 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY F 473 " --> pdb=" O LYS F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 513 removed outlier: 3.581A pdb=" N ILE F 510 " --> pdb=" O TYR F 506 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE F 513 " --> pdb=" O GLN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 555 removed outlier: 4.185A pdb=" N GLU F 552 " --> pdb=" O GLY F 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.506A pdb=" N GLY G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 290 removed outlier: 3.589A pdb=" N ARG G 290 " --> pdb=" O THR G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.997A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 471 Processing helix chain 'G' and resid 502 through 505 removed outlier: 4.225A pdb=" N ASP G 505 " --> pdb=" O SER G 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 502 through 505' Processing helix chain 'G' and resid 506 through 514 removed outlier: 3.654A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER G 514 " --> pdb=" O ILE G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 555 removed outlier: 4.040A pdb=" N GLU G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 34 Processing helix chain 'Z' and resid 39 through 50 removed outlier: 3.949A pdb=" N LYS Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 62 removed outlier: 3.765A pdb=" N THR Z 62 " --> pdb=" O LYS Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 67 through 72 removed outlier: 4.014A pdb=" N ILE Z 71 " --> pdb=" O TYR Z 67 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU Z 72 " --> pdb=" O ASP Z 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 67 through 72' Processing helix chain 'Z' and resid 77 through 88 Processing helix chain 'Z' and resid 122 through 133 removed outlier: 3.540A pdb=" N ILE Z 133 " --> pdb=" O PHE Z 129 " (cutoff:3.500A) Processing helix chain 'Z' and resid 223 through 236 Processing helix chain 'Z' and resid 237 through 239 No H-bonds generated for 'chain 'Z' and resid 237 through 239' Processing helix chain 'Z' and resid 243 through 256 Processing helix chain 'Z' and resid 257 through 267 removed outlier: 4.644A pdb=" N ASN Z 263 " --> pdb=" O THR Z 259 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU Z 265 " --> pdb=" O ILE Z 261 " (cutoff:3.500A) Processing helix chain 'Z' and resid 268 through 273 Processing helix chain 'Z' and resid 275 through 291 Processing helix chain 'Z' and resid 306 through 310 removed outlier: 3.807A pdb=" N GLY Z 310 " --> pdb=" O GLN Z 307 " (cutoff:3.500A) Processing helix chain 'Z' and resid 315 through 319 Processing helix chain 'Z' and resid 322 through 333 removed outlier: 3.684A pdb=" N ILE Z 326 " --> pdb=" O LYS Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 375 through 379 removed outlier: 3.678A pdb=" N ILE Z 379 " --> pdb=" O LEU Z 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 311 removed outlier: 5.003A pdb=" N VAL A 300 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 398 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 392 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 311 removed outlier: 5.003A pdb=" N VAL A 300 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 398 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 392 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.838A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A 482 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN A 411 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N THR A 480 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 413 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 478 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 520 Processing sheet with id=AA7, first strand: chain 'B' and resid 235 through 237 Processing sheet with id=AA8, first strand: chain 'B' and resid 299 through 311 removed outlier: 4.624A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 299 through 311 removed outlier: 4.624A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 403 through 406 removed outlier: 7.030A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 422 through 423 removed outlier: 3.744A pdb=" N GLN B 482 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN B 411 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N THR B 480 " --> pdb=" O ASN B 411 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL B 413 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU B 478 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 514 through 519 Processing sheet with id=AB4, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AB5, first strand: chain 'C' and resid 299 through 311 removed outlier: 4.636A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 403 through 405 removed outlier: 6.313A pdb=" N LYS C 405 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN C 431 " --> pdb=" O LYS C 405 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 417 through 422 removed outlier: 6.934A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 514 through 519 Processing sheet with id=AB9, first strand: chain 'D' and resid 235 through 237 Processing sheet with id=AC1, first strand: chain 'D' and resid 298 through 311 removed outlier: 4.661A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 405 through 406 removed outlier: 3.521A pdb=" N VAL D 406 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 430 " --> pdb=" O VAL D 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 417 through 422 removed outlier: 4.795A pdb=" N THR D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU D 414 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 489 through 491 removed outlier: 4.426A pdb=" N ASN D 491 " --> pdb=" O GLN D 495 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLN D 495 " --> pdb=" O ASN D 491 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 514 through 520 Processing sheet with id=AC6, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AC7, first strand: chain 'E' and resid 298 through 311 removed outlier: 4.976A pdb=" N VAL E 300 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR E 398 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN E 392 " --> pdb=" O LYS E 306 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN E 397 " --> pdb=" O ASP E 437 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP E 437 " --> pdb=" O ASN E 397 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 298 through 311 removed outlier: 4.976A pdb=" N VAL E 300 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR E 398 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN E 392 " --> pdb=" O LYS E 306 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 418 through 422 removed outlier: 3.835A pdb=" N SER E 420 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 515 through 520 Processing sheet with id=AD2, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AD3, first strand: chain 'F' and resid 298 through 311 removed outlier: 4.453A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 298 through 311 removed outlier: 4.453A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 403 through 406 removed outlier: 6.892A pdb=" N TYR F 404 " --> pdb=" O ASN F 432 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 423 removed outlier: 3.860A pdb=" N GLN F 482 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN F 411 " --> pdb=" O THR F 480 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N THR F 480 " --> pdb=" O ASN F 411 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL F 413 " --> pdb=" O LEU F 478 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU F 478 " --> pdb=" O VAL F 413 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 514 through 520 Processing sheet with id=AD8, first strand: chain 'G' and resid 236 through 238 Processing sheet with id=AD9, first strand: chain 'G' and resid 298 through 311 removed outlier: 4.492A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.822A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 515 through 520 Processing sheet with id=AE3, first strand: chain 'Z' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA Z 210 " --> pdb=" O LEU Z 162 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL Z 214 " --> pdb=" O LYS Z 166 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS Z 205 " --> pdb=" O VAL Z 201 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL Z 201 " --> pdb=" O LYS Z 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR Z 207 " --> pdb=" O ARG Z 199 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG Z 199 " --> pdb=" O TYR Z 207 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS Z 209 " --> pdb=" O ILE Z 197 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE Z 197 " --> pdb=" O LYS Z 209 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU Z 211 " --> pdb=" O ASP Z 195 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER Z 213 " --> pdb=" O LYS Z 193 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS Z 193 " --> pdb=" O SER Z 213 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER Z 191 " --> pdb=" O VAL Z 215 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 143 through 146 Processing sheet with id=AE5, first strand: chain 'Z' and resid 298 through 304 removed outlier: 3.970A pdb=" N ILE Z 361 " --> pdb=" O SER Z 304 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL Z 362 " --> pdb=" O LEU Z 412 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL Z 414 " --> pdb=" O VAL Z 362 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR Z 366 " --> pdb=" O ALA Z 416 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU Z 418 " --> pdb=" O THR Z 366 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE Z 409 " --> pdb=" O LYS Z 405 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS Z 405 " --> pdb=" O ILE Z 409 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS Z 411 " --> pdb=" O SER Z 403 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER Z 403 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE Z 413 " --> pdb=" O ILE Z 401 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE Z 401 " --> pdb=" O ILE Z 413 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP Z 415 " --> pdb=" O ASN Z 399 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 344 through 347 488 hydrogen bonds defined for protein. 1284 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: 5.28 Time building geometry restraints manager: 6.44 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: 5043 1.33 - 1.45: 2853 1.45 - 1.57: 10316 1.57 - 1.69: 0 1.69 - 1.80: 52 Bond restraints: 18264 Sorted by residual: bond pdb=" CA TRP F 503 " pdb=" C TRP F 503 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.80e-02 3.09e+03 1.62e+01 bond pdb=" CA TRP D 503 " pdb=" C TRP D 503 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.80e-02 3.09e+03 1.48e+01 bond pdb=" C GLN Z 118 " pdb=" N ASN Z 119 " ideal model delta sigma weight residual 1.332 1.308 0.025 1.40e-02 5.10e+03 3.11e+00 bond pdb=" C THR D 400 " pdb=" N ALA D 401 " ideal model delta sigma weight residual 1.340 1.238 0.102 5.87e-02 2.90e+02 3.01e+00 bond pdb=" CG LEU E 433 " pdb=" CD2 LEU E 433 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.95e+00 ... (remaining 18259 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.18: 400 106.18 - 113.18: 9896 113.18 - 120.18: 6522 120.18 - 127.18: 7812 127.18 - 134.18: 123 Bond angle restraints: 24753 Sorted by residual: angle pdb=" N GLY B 485 " pdb=" CA GLY B 485 " pdb=" C GLY B 485 " ideal model delta sigma weight residual 110.77 115.48 -4.71 1.59e+00 3.96e-01 8.79e+00 angle pdb=" CA TYR B 439 " pdb=" CB TYR B 439 " pdb=" CG TYR B 439 " ideal model delta sigma weight residual 113.90 108.81 5.09 1.80e+00 3.09e-01 8.00e+00 angle pdb=" C TYR D 439 " pdb=" N PRO D 440 " pdb=" CA PRO D 440 " ideal model delta sigma weight residual 120.79 117.18 3.61 1.30e+00 5.92e-01 7.69e+00 angle pdb=" N ILE A 507 " pdb=" CA ILE A 507 " pdb=" C ILE A 507 " ideal model delta sigma weight residual 113.39 109.31 4.08 1.47e+00 4.63e-01 7.69e+00 angle pdb=" C LEU C 414 " pdb=" N ASP C 415 " pdb=" CA ASP C 415 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.65e+00 ... (remaining 24748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 9944 17.66 - 35.32: 988 35.32 - 52.99: 170 52.99 - 70.65: 29 70.65 - 88.31: 14 Dihedral angle restraints: 11145 sinusoidal: 4453 harmonic: 6692 Sorted by residual: dihedral pdb=" CA LYS C 490 " pdb=" C LYS C 490 " pdb=" N ASN C 491 " pdb=" CA ASN C 491 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA MET C 304 " pdb=" C MET C 304 " pdb=" N GLU C 305 " pdb=" CA GLU C 305 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TYR E 404 " pdb=" C TYR E 404 " pdb=" N LYS E 405 " pdb=" CA LYS E 405 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 11142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1596 0.036 - 0.072: 752 0.072 - 0.109: 302 0.109 - 0.145: 95 0.145 - 0.181: 7 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CA ASN B 432 " pdb=" N ASN B 432 " pdb=" C ASN B 432 " pdb=" CB ASN B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA TYR D 404 " pdb=" N TYR D 404 " pdb=" C TYR D 404 " pdb=" CB TYR D 404 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ASN C 432 " pdb=" N ASN C 432 " pdb=" C ASN C 432 " pdb=" CB ASN C 432 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 2749 not shown) Planarity restraints: 3251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 291 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO F 292 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 292 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 292 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Z 273 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO Z 274 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO Z 274 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO Z 274 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 434 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO D 435 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 435 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 435 " 0.031 5.00e-02 4.00e+02 ... (remaining 3248 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1693 2.72 - 3.27: 18050 3.27 - 3.81: 25949 3.81 - 4.36: 30789 4.36 - 4.90: 55070 Nonbonded interactions: 131551 Sorted by model distance: nonbonded pdb=" OD1 ASN B 450 " pdb=" OG1 THR B 451 " model vdw 2.181 2.440 nonbonded pdb=" OD2 ASP Z 219 " pdb=" OG1 THR Z 299 " model vdw 2.199 2.440 nonbonded pdb=" O PHE Z 320 " pdb=" OG1 THR Z 410 " model vdw 2.202 2.440 nonbonded pdb=" ND2 ASN D 260 " pdb=" O LYS D 541 " model vdw 2.211 2.520 nonbonded pdb=" OE1 GLN E 482 " pdb=" OH TYR F 439 " model vdw 2.217 2.440 ... (remaining 131546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 224 through 556 or resid 901 through 902)) selection = (chain 'B' and (resid 224 through 556 or resid 901 through 902)) selection = chain 'C' selection = (chain 'D' and (resid 224 through 556 or resid 901 through 902)) selection = (chain 'E' and (resid 224 through 556 or resid 901 through 902)) selection = (chain 'F' and (resid 224 through 556 or resid 901 through 902)) selection = (chain 'G' and (resid 224 through 556 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 3.340 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 44.340 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 0.007 0.102 18264 Z= 0.459 Angle : 0.749 8.322 24753 Z= 0.411 Chirality : 0.049 0.181 2752 Planarity : 0.005 0.058 3251 Dihedral : 14.400 88.309 6867 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Rotamer: Outliers : 0.25 % Allowed : 11.38 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (0.13), residues: 2263 helix: -3.62 (0.15), residues: 473 sheet: -2.77 (0.19), residues: 507 loop : -4.11 (0.13), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 503 HIS 0.001 0.001 HIS Z 392 PHE 0.024 0.002 PHE B 487 TYR 0.020 0.002 TYR E 257 ARG 0.005 0.001 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 201 average time/residue: 0.3255 time to fit residues: 97.8618 Evaluate side-chains 140 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 2.144 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1575 time to fit residues: 3.5059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 68 optimal weight: 0.0170 chunk 107 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN C 509 GLN D 252 GLN D 427 ASN D 466 GLN D 509 GLN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN G 432 ASN Z 251 ASN ** Z 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18264 Z= 0.173 Angle : 0.575 7.225 24753 Z= 0.306 Chirality : 0.045 0.161 2752 Planarity : 0.005 0.050 3251 Dihedral : 5.037 18.901 2471 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.30 % Allowed : 16.60 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.14), residues: 2263 helix: -2.42 (0.19), residues: 486 sheet: -2.32 (0.19), residues: 511 loop : -3.56 (0.14), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 503 HIS 0.002 0.001 HIS Z 392 PHE 0.013 0.001 PHE B 487 TYR 0.020 0.001 TYR B 396 ARG 0.006 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 203 average time/residue: 0.2681 time to fit residues: 86.4609 Evaluate side-chains 168 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 2.040 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1568 time to fit residues: 7.3651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18264 Z= 0.294 Angle : 0.614 7.629 24753 Z= 0.327 Chirality : 0.046 0.160 2752 Planarity : 0.005 0.045 3251 Dihedral : 5.118 19.154 2471 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 2.91 % Allowed : 18.91 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.15), residues: 2263 helix: -2.03 (0.20), residues: 492 sheet: -2.12 (0.20), residues: 511 loop : -3.37 (0.14), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 503 HIS 0.002 0.001 HIS Z 392 PHE 0.018 0.002 PHE B 487 TYR 0.021 0.002 TYR B 396 ARG 0.007 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 164 time to evaluate : 2.127 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 31 residues processed: 209 average time/residue: 0.2639 time to fit residues: 88.5704 Evaluate side-chains 182 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 2.161 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1603 time to fit residues: 12.2938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 195 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 18264 Z= 0.325 Angle : 0.636 8.410 24753 Z= 0.338 Chirality : 0.046 0.184 2752 Planarity : 0.005 0.045 3251 Dihedral : 5.192 18.871 2471 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 2.16 % Allowed : 21.87 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.15), residues: 2263 helix: -1.78 (0.21), residues: 492 sheet: -1.93 (0.20), residues: 515 loop : -3.31 (0.15), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 503 HIS 0.003 0.001 HIS Z 392 PHE 0.019 0.002 PHE B 487 TYR 0.017 0.002 TYR F 261 ARG 0.006 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 2.147 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 24 residues processed: 189 average time/residue: 0.2603 time to fit residues: 79.9836 Evaluate side-chains 165 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1681 time to fit residues: 10.3813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 162 optimal weight: 0.0870 chunk 90 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 0.6980 chunk 196 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN C 509 GLN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18264 Z= 0.261 Angle : 0.596 7.361 24753 Z= 0.318 Chirality : 0.045 0.177 2752 Planarity : 0.004 0.044 3251 Dihedral : 4.986 18.789 2471 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.16 % Allowed : 23.12 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.15), residues: 2263 helix: -1.50 (0.22), residues: 491 sheet: -1.77 (0.20), residues: 515 loop : -3.20 (0.15), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 503 HIS 0.002 0.001 HIS Z 392 PHE 0.017 0.001 PHE B 487 TYR 0.014 0.001 TYR E 257 ARG 0.004 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 159 time to evaluate : 2.030 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 24 residues processed: 195 average time/residue: 0.2757 time to fit residues: 86.0935 Evaluate side-chains 168 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1845 time to fit residues: 10.9181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 0.1980 chunk 196 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 140 GLN Z 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18264 Z= 0.157 Angle : 0.539 7.512 24753 Z= 0.286 Chirality : 0.044 0.157 2752 Planarity : 0.004 0.074 3251 Dihedral : 4.561 18.060 2471 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.50 % Allowed : 23.97 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.16), residues: 2263 helix: -1.15 (0.23), residues: 492 sheet: -1.63 (0.21), residues: 515 loop : -3.00 (0.15), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 503 HIS 0.001 0.001 HIS Z 392 PHE 0.012 0.001 PHE B 487 TYR 0.010 0.001 TYR C 464 ARG 0.006 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 2.184 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 195 average time/residue: 0.2844 time to fit residues: 89.4655 Evaluate side-chains 173 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1781 time to fit residues: 9.8048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18264 Z= 0.240 Angle : 0.578 8.169 24753 Z= 0.307 Chirality : 0.045 0.171 2752 Planarity : 0.004 0.062 3251 Dihedral : 4.719 18.466 2471 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.71 % Allowed : 24.12 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.16), residues: 2263 helix: -1.13 (0.23), residues: 490 sheet: -1.48 (0.21), residues: 511 loop : -3.00 (0.15), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 503 HIS 0.003 0.001 HIS Z 206 PHE 0.016 0.001 PHE B 487 TYR 0.013 0.001 TYR F 261 ARG 0.007 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 1.996 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 183 average time/residue: 0.2660 time to fit residues: 78.1394 Evaluate side-chains 165 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.966 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1601 time to fit residues: 8.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 107 optimal weight: 0.0000 chunk 20 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18264 Z= 0.142 Angle : 0.523 6.925 24753 Z= 0.276 Chirality : 0.043 0.166 2752 Planarity : 0.004 0.052 3251 Dihedral : 4.349 17.648 2471 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.70 % Allowed : 24.87 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.16), residues: 2263 helix: -0.85 (0.23), residues: 488 sheet: -1.40 (0.21), residues: 515 loop : -2.82 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 503 HIS 0.002 0.001 HIS Z 206 PHE 0.011 0.001 PHE B 487 TYR 0.011 0.001 TYR F 464 ARG 0.008 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 182 average time/residue: 0.2759 time to fit residues: 79.8119 Evaluate side-chains 161 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 2.087 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1699 time to fit residues: 4.8550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 0.0970 chunk 190 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 183 optimal weight: 20.0000 chunk 191 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18264 Z= 0.177 Angle : 0.554 8.097 24753 Z= 0.291 Chirality : 0.044 0.189 2752 Planarity : 0.004 0.051 3251 Dihedral : 4.390 17.891 2471 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.35 % Allowed : 25.88 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.16), residues: 2263 helix: -0.78 (0.23), residues: 490 sheet: -1.33 (0.21), residues: 519 loop : -2.78 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 245 HIS 0.002 0.001 HIS Z 206 PHE 0.013 0.001 PHE B 487 TYR 0.015 0.001 TYR D 506 ARG 0.008 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 164 average time/residue: 0.2743 time to fit residues: 72.4289 Evaluate side-chains 157 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 2.067 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1674 time to fit residues: 3.7205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 225 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18264 Z= 0.178 Angle : 0.553 8.665 24753 Z= 0.290 Chirality : 0.044 0.179 2752 Planarity : 0.004 0.050 3251 Dihedral : 4.383 17.777 2471 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.15 % Allowed : 26.28 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.16), residues: 2263 helix: -0.69 (0.24), residues: 489 sheet: -1.31 (0.21), residues: 519 loop : -2.71 (0.15), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 245 HIS 0.002 0.001 HIS Z 206 PHE 0.013 0.001 PHE B 487 TYR 0.015 0.001 TYR D 506 ARG 0.007 0.000 ARG F 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 160 average time/residue: 0.2761 time to fit residues: 71.0448 Evaluate side-chains 155 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1672 time to fit residues: 3.1297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 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 = 0.3420 r_free = 0.3420 target = 0.116385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097845 restraints weight = 35239.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.099528 restraints weight = 22584.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100718 restraints weight = 16698.991| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18264 Z= 0.161 Angle : 0.544 8.833 24753 Z= 0.285 Chirality : 0.044 0.181 2752 Planarity : 0.004 0.048 3251 Dihedral : 4.281 17.462 2471 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.30 % Allowed : 26.48 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.16), residues: 2263 helix: -0.62 (0.24), residues: 489 sheet: -1.26 (0.21), residues: 519 loop : -2.66 (0.15), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 245 HIS 0.002 0.001 HIS Z 206 PHE 0.012 0.001 PHE B 487 TYR 0.017 0.001 TYR D 506 ARG 0.008 0.000 ARG B 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.78 seconds wall clock time: 53 minutes 27.45 seconds (3207.45 seconds total)