Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 03:08:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/05_2023/8sal_40273_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/05_2023/8sal_40273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/05_2023/8sal_40273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/05_2023/8sal_40273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/05_2023/8sal_40273_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/05_2023/8sal_40273_neut.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 134 5.16 5 C 11596 2.51 5 N 3211 2.21 5 O 3494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 418": "OD1" <-> "OD2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 418": "OD1" <-> "OD2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 60": "OD1" <-> "OD2" Residue "I TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 418": "OD1" <-> "OD2" Residue "L ASP 60": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 18435 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3508 Classifications: {'peptide': 448} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 425} Chain breaks: 1 Chain: "B" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 904 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 2 Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Chain: "E" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3425 Classifications: {'peptide': 437} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 413} Chain breaks: 2 Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 900 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Chain: "I" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3503 Classifications: {'peptide': 447} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain breaks: 1 Chain: "J" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 945 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Time building chain proxies: 9.52, per 1000 atoms: 0.52 Number of scatterers: 18435 At special positions: 0 Unit cell: (143.91, 150.306, 112.996, 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 134 16.00 O 3494 8.00 N 3211 7.00 C 11596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 165 " distance=2.02 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 187 " - pdb=" SG CYS A 216 " distance=2.04 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 44 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 165 " distance=2.02 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 124 " distance=2.03 Simple disulfide: pdb=" SG CYS E 187 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 197 " - pdb=" SG CYS E 208 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 345 " - pdb=" SG CYS E 406 " distance=2.03 Simple disulfide: pdb=" SG CYS E 352 " - pdb=" SG CYS E 379 " distance=2.03 Simple disulfide: pdb=" SG CYS F 562 " - pdb=" SG CYS F 568 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 44 " distance=2.02 Simple disulfide: pdb=" SG CYS I 89 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 96 " - pdb=" SG CYS I 165 " distance=2.02 Simple disulfide: pdb=" SG CYS I 101 " - pdb=" SG CYS I 124 " distance=2.03 Simple disulfide: pdb=" SG CYS I 187 " - pdb=" SG CYS I 216 " distance=2.03 Simple disulfide: pdb=" SG CYS I 197 " - pdb=" SG CYS I 208 " distance=2.03 Simple disulfide: pdb=" SG CYS I 265 " - pdb=" SG CYS I 299 " distance=2.03 Simple disulfide: pdb=" SG CYS I 345 " - pdb=" SG CYS I 406 " distance=2.03 Simple disulfide: pdb=" SG CYS I 352 " - pdb=" SG CYS I 379 " distance=2.03 Simple disulfide: pdb=" SG CYS J 562 " - pdb=" SG CYS J 568 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.34 Conformation dependent library (CDL) restraints added in 3.2 seconds 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4322 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 48 sheets defined 22.1% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 69 through 87 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 304 through 321 removed outlier: 3.929A pdb=" N HIS A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.760A pdb=" N PHE A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'B' and resid 485 through 491 Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.759A pdb=" N MET B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 509 removed outlier: 4.585A pdb=" N GLN B 504 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 536 removed outlier: 3.777A pdb=" N GLY B 536 " --> pdb=" O THR B 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 536' Processing helix chain 'B' and resid 537 through 560 removed outlier: 4.191A pdb=" N GLN B 541 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 587 Processing helix chain 'B' and resid 591 through 601 removed outlier: 3.545A pdb=" N TRP B 595 " --> pdb=" O THR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 619 removed outlier: 3.860A pdb=" N GLN B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.769A pdb=" N GLN C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 69 through 87 Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 164 through 167 Processing helix chain 'E' and resid 304 through 321 removed outlier: 4.001A pdb=" N HIS E 311 " --> pdb=" O ASN E 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU E 312 " --> pdb=" O LYS E 308 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.759A pdb=" N PHE E 358 " --> pdb=" O THR E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 366 Processing helix chain 'E' and resid 436 through 443 Processing helix chain 'E' and resid 444 through 446 No H-bonds generated for 'chain 'E' and resid 444 through 446' Processing helix chain 'F' and resid 486 through 491 Processing helix chain 'F' and resid 493 through 498 Processing helix chain 'F' and resid 500 through 509 removed outlier: 4.401A pdb=" N GLN F 504 " --> pdb=" O THR F 500 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA F 505 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU F 509 " --> pdb=" O ALA F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 537 Processing helix chain 'F' and resid 538 through 560 removed outlier: 3.728A pdb=" N ALA F 542 " --> pdb=" O LYS F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 588 removed outlier: 3.560A pdb=" N ILE F 586 " --> pdb=" O ASN F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 601 removed outlier: 3.501A pdb=" N TRP F 595 " --> pdb=" O THR F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 619 Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.869A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 69 through 87 Processing helix chain 'I' and resid 92 through 96 Processing helix chain 'I' and resid 117 through 119 No H-bonds generated for 'chain 'I' and resid 117 through 119' Processing helix chain 'I' and resid 164 through 167 Processing helix chain 'I' and resid 304 through 321 removed outlier: 3.921A pdb=" N HIS I 311 " --> pdb=" O ASN I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 340 Processing helix chain 'I' and resid 354 through 359 removed outlier: 3.812A pdb=" N PHE I 358 " --> pdb=" O THR I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 366 Processing helix chain 'I' and resid 427 through 431 Processing helix chain 'I' and resid 436 through 443 Processing helix chain 'I' and resid 444 through 446 No H-bonds generated for 'chain 'I' and resid 444 through 446' Processing helix chain 'J' and resid 485 through 491 removed outlier: 3.666A pdb=" N ALA J 489 " --> pdb=" O GLY J 485 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA J 490 " --> pdb=" O PHE J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 493 through 500 removed outlier: 3.576A pdb=" N ALA J 497 " --> pdb=" O THR J 493 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET J 499 " --> pdb=" O GLY J 495 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR J 500 " --> pdb=" O ALA J 496 " (cutoff:3.500A) Processing helix chain 'J' and resid 500 through 508 removed outlier: 3.646A pdb=" N GLN J 504 " --> pdb=" O THR J 500 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN J 507 " --> pdb=" O VAL J 503 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 536 removed outlier: 3.824A pdb=" N GLY J 536 " --> pdb=" O THR J 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 533 through 536' Processing helix chain 'J' and resid 537 through 560 removed outlier: 3.729A pdb=" N GLN J 541 " --> pdb=" O ILE J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 588 Processing helix chain 'J' and resid 591 through 601 removed outlier: 3.677A pdb=" N ASN J 601 " --> pdb=" O LYS J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 610 through 618 Processing helix chain 'K' and resid 60 through 64 removed outlier: 3.971A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 3.667A pdb=" N ILE A 194 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 25 removed outlier: 3.634A pdb=" N PHE A 23 " --> pdb=" O CYS A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 64 Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 230 removed outlier: 6.332A pdb=" N LEU A 229 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N THR A 405 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N ILE A 263 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N LYS A 407 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N VAL A 261 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ASN A 409 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N THR A 259 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR A 411 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 228 through 230 removed outlier: 6.332A pdb=" N LEU A 229 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N THR A 405 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N ILE A 263 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N LYS A 407 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N VAL A 261 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ASN A 409 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N THR A 259 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR A 411 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 299 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 377 " --> pdb=" O CYS A 299 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 272 through 277 removed outlier: 6.794A pdb=" N THR A 272 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 343 removed outlier: 3.520A pdb=" N PHE A 343 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A 349 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 382 " --> pdb=" O PHE A 349 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 384 through 386 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.374A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 94 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.374A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 107 " --> pdb=" O TYR C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.421A pdb=" N LEU D 11 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.421A pdb=" N LEU D 11 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 15 through 16 removed outlier: 3.760A pdb=" N ILE E 194 " --> pdb=" O VAL E 214 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 23 through 25 removed outlier: 3.522A pdb=" N PHE E 23 " --> pdb=" O CYS E 187 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR E 186 " --> pdb=" O HIS E 218 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS E 218 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 61 through 64 Processing sheet with id=AC2, first strand: chain 'E' and resid 141 through 144 Processing sheet with id=AC3, first strand: chain 'E' and resid 127 through 129 Processing sheet with id=AC4, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.299A pdb=" N LEU E 229 " --> pdb=" O THR E 411 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N THR E 405 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 11.776A pdb=" N ILE E 263 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N LYS E 407 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N VAL E 261 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N ASN E 409 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N THR E 259 " --> pdb=" O ASN E 409 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR E 411 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.299A pdb=" N LEU E 229 " --> pdb=" O THR E 411 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N THR E 405 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 11.776A pdb=" N ILE E 263 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N LYS E 407 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N VAL E 261 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N ASN E 409 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N THR E 259 " --> pdb=" O ASN E 409 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR E 411 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS E 299 " --> pdb=" O LEU E 377 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 272 through 277 removed outlier: 6.814A pdb=" N THR E 272 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 341 through 343 removed outlier: 3.836A pdb=" N PHE E 349 " --> pdb=" O LYS E 382 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 385 through 386 Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'G' and resid 47 through 51 removed outlier: 6.205A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG G 94 " --> pdb=" O HIS G 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 47 through 51 removed outlier: 6.205A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.516A pdb=" N ARG H 24 " --> pdb=" O THR H 5 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.395A pdb=" N LEU H 11 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.395A pdb=" N LEU H 11 " --> pdb=" O GLN H 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 9 through 16 removed outlier: 5.933A pdb=" N TYR I 10 " --> pdb=" O GLY I 457 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLY I 457 " --> pdb=" O TYR I 10 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL I 14 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE I 453 " --> pdb=" O VAL I 14 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS I 16 " --> pdb=" O VAL I 451 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL I 451 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE I 194 " --> pdb=" O VAL I 214 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 23 through 25 Processing sheet with id=AD8, first strand: chain 'I' and resid 61 through 64 Processing sheet with id=AD9, first strand: chain 'I' and resid 141 through 144 Processing sheet with id=AE1, first strand: chain 'I' and resid 127 through 129 Processing sheet with id=AE2, first strand: chain 'I' and resid 228 through 230 removed outlier: 6.337A pdb=" N LEU I 229 " --> pdb=" O THR I 411 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N THR I 405 " --> pdb=" O ILE I 263 " (cutoff:3.500A) removed outlier: 11.758A pdb=" N ILE I 263 " --> pdb=" O THR I 405 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N LYS I 407 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 11.111A pdb=" N VAL I 261 " --> pdb=" O LYS I 407 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N ASN I 409 " --> pdb=" O THR I 259 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N THR I 259 " --> pdb=" O ASN I 409 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR I 411 " --> pdb=" O LEU I 257 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 228 through 230 removed outlier: 6.337A pdb=" N LEU I 229 " --> pdb=" O THR I 411 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N THR I 405 " --> pdb=" O ILE I 263 " (cutoff:3.500A) removed outlier: 11.758A pdb=" N ILE I 263 " --> pdb=" O THR I 405 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N LYS I 407 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 11.111A pdb=" N VAL I 261 " --> pdb=" O LYS I 407 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N ASN I 409 " --> pdb=" O THR I 259 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N THR I 259 " --> pdb=" O ASN I 409 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR I 411 " --> pdb=" O LEU I 257 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS I 299 " --> pdb=" O LEU I 377 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 272 through 277 removed outlier: 6.738A pdb=" N THR I 272 " --> pdb=" O GLY I 288 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 341 through 343 removed outlier: 4.041A pdb=" N PHE I 349 " --> pdb=" O LYS I 382 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS I 382 " --> pdb=" O PHE I 349 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 384 through 386 Processing sheet with id=AE7, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.421A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG K 94 " --> pdb=" O HIS K 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.421A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR K 107 " --> pdb=" O TYR K 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.399A pdb=" N LEU L 11 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.399A pdb=" N LEU L 11 " --> pdb=" O GLN L 105 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1623 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: 6.41 Time building geometry restraints manager: 7.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 6478 1.37 - 1.53: 10551 1.53 - 1.69: 1630 1.69 - 1.84: 179 1.84 - 2.00: 3 Bond restraints: 18841 Sorted by residual: bond pdb=" CB CYS F 569 " pdb=" SG CYS F 569 " ideal model delta sigma weight residual 1.808 1.998 -0.190 3.30e-02 9.18e+02 3.30e+01 bond pdb=" CB CYS B 569 " pdb=" SG CYS B 569 " ideal model delta sigma weight residual 1.808 1.995 -0.187 3.30e-02 9.18e+02 3.21e+01 bond pdb=" CB CYS J 569 " pdb=" SG CYS J 569 " ideal model delta sigma weight residual 1.808 1.990 -0.182 3.30e-02 9.18e+02 3.04e+01 bond pdb=" C ASP I 48 " pdb=" N PRO I 49 " ideal model delta sigma weight residual 1.331 1.362 -0.030 7.90e-03 1.60e+04 1.45e+01 bond pdb=" C VAL A 458 " pdb=" N ALA A 459 " ideal model delta sigma weight residual 1.329 1.364 -0.035 1.40e-02 5.10e+03 6.31e+00 ... (remaining 18836 not shown) Histogram of bond angle deviations from ideal: 97.27 - 104.63: 322 104.63 - 111.99: 8996 111.99 - 119.36: 6564 119.36 - 126.72: 9318 126.72 - 134.08: 370 Bond angle restraints: 25570 Sorted by residual: angle pdb=" CA CYS F 569 " pdb=" CB CYS F 569 " pdb=" SG CYS F 569 " ideal model delta sigma weight residual 114.40 128.63 -14.23 2.30e+00 1.89e-01 3.83e+01 angle pdb=" N THR J 570 " pdb=" CA THR J 570 " pdb=" C THR J 570 " ideal model delta sigma weight residual 112.89 119.91 -7.02 1.24e+00 6.50e-01 3.20e+01 angle pdb=" N THR B 570 " pdb=" CA THR B 570 " pdb=" C THR B 570 " ideal model delta sigma weight residual 112.68 119.33 -6.65 1.33e+00 5.65e-01 2.50e+01 angle pdb=" N LEU F 609 " pdb=" CA LEU F 609 " pdb=" C LEU F 609 " ideal model delta sigma weight residual 111.71 117.17 -5.46 1.15e+00 7.56e-01 2.26e+01 angle pdb=" N LYS A 422 " pdb=" CA LYS A 422 " pdb=" C LYS A 422 " ideal model delta sigma weight residual 108.34 100.64 7.70 1.64e+00 3.72e-01 2.21e+01 ... (remaining 25565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10284 17.97 - 35.94: 830 35.94 - 53.91: 141 53.91 - 71.88: 29 71.88 - 89.85: 21 Dihedral angle restraints: 11305 sinusoidal: 4567 harmonic: 6738 Sorted by residual: dihedral pdb=" CA THR I 421 " pdb=" C THR I 421 " pdb=" N LYS I 422 " pdb=" CA LYS I 422 " ideal model delta harmonic sigma weight residual 180.00 131.22 48.78 0 5.00e+00 4.00e-02 9.52e+01 dihedral pdb=" CA THR A 421 " pdb=" C THR A 421 " pdb=" N LYS A 422 " pdb=" CA LYS A 422 " ideal model delta harmonic sigma weight residual 180.00 134.26 45.74 0 5.00e+00 4.00e-02 8.37e+01 dihedral pdb=" CA LYS A 33 " pdb=" C LYS A 33 " pdb=" N GLU A 34 " pdb=" CA GLU A 34 " ideal model delta harmonic sigma weight residual 180.00 140.25 39.75 0 5.00e+00 4.00e-02 6.32e+01 ... (remaining 11302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2165 0.049 - 0.099: 434 0.099 - 0.148: 196 0.148 - 0.197: 18 0.197 - 0.246: 1 Chirality restraints: 2814 Sorted by residual: chirality pdb=" CG LEU A 4 " pdb=" CB LEU A 4 " pdb=" CD1 LEU A 4 " pdb=" CD2 LEU A 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE B 567 " pdb=" N ILE B 567 " pdb=" C ILE B 567 " pdb=" CB ILE B 567 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA ILE J 567 " pdb=" N ILE J 567 " pdb=" C ILE J 567 " pdb=" CB ILE J 567 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 2811 not shown) Planarity restraints: 3281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 9 " -0.037 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR I 9 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR I 9 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR I 9 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR I 9 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR I 9 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR I 9 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR I 9 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 459 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ALA E 459 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA E 459 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO E 460 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 459 " -0.047 5.00e-02 4.00e+02 7.35e-02 8.63e+00 pdb=" N PRO E 460 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO E 460 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 460 " -0.040 5.00e-02 4.00e+02 ... (remaining 3278 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 281 2.63 - 3.20: 17579 3.20 - 3.77: 28336 3.77 - 4.33: 38450 4.33 - 4.90: 62494 Nonbonded interactions: 147140 Sorted by model distance: nonbonded pdb=" OG1 THR A 416 " pdb=" O GLU A 428 " model vdw 2.065 2.440 nonbonded pdb=" OE1 GLU I 303 " pdb=" OG SER I 371 " model vdw 2.096 2.440 nonbonded pdb=" OE1 GLU E 303 " pdb=" OG SER E 371 " model vdw 2.097 2.440 nonbonded pdb=" OE1 GLU A 303 " pdb=" OG SER A 371 " model vdw 2.098 2.440 nonbonded pdb=" O ASN E 440 " pdb=" OG SER E 443 " model vdw 2.111 2.440 ... (remaining 147135 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 3 through 418 or resid 431 through 458)) selection = (chain 'E' and resid 3 through 458) selection = (chain 'I' and (resid 3 through 418 or resid 431 through 458)) } ncs_group { reference = (chain 'B' and (resid 485 through 510 or resid 533 through 619)) selection = (chain 'F' and (resid 485 through 561 or resid 567 through 619)) selection = (chain 'J' and (resid 485 through 510 or resid 533 through 561 or resid 567 thro \ ugh 619)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } 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: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.110 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 48.030 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.005 0.190 18841 Z= 0.328 Angle : 0.889 14.235 25570 Z= 0.498 Chirality : 0.049 0.246 2814 Planarity : 0.005 0.073 3281 Dihedral : 13.673 89.852 6869 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.45 % Favored : 91.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -2.31 (0.17), residues: 2297 helix: -0.35 (0.26), residues: 392 sheet: -1.58 (0.19), residues: 611 loop : -1.90 (0.16), residues: 1294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 678 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.3460 time to fit residues: 335.8687 Evaluate side-chains 406 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 208 optimal weight: 30.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 42 HIS A 75 HIS ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN A 423 ASN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 3 ASN E 75 HIS E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN E 318 GLN H 38 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 305 GLN I 423 ASN K 64 GLN L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 18841 Z= 0.234 Angle : 0.725 7.819 25570 Z= 0.391 Chirality : 0.047 0.223 2814 Planarity : 0.005 0.087 3281 Dihedral : 6.835 35.833 2530 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.53 % Favored : 93.34 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.96 (0.17), residues: 2297 helix: -0.50 (0.25), residues: 419 sheet: -1.32 (0.21), residues: 593 loop : -1.56 (0.17), residues: 1285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 499 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 0 residues processed: 510 average time/residue: 0.3389 time to fit residues: 255.0708 Evaluate side-chains 315 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.230 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 73 GLN A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 42 HIS E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN G 64 GLN H 38 GLN I 73 GLN I 75 HIS I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 271 ASN ** I 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 18841 Z= 0.199 Angle : 0.702 10.482 25570 Z= 0.374 Chirality : 0.046 0.193 2814 Planarity : 0.005 0.048 3281 Dihedral : 6.578 35.008 2530 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.05 % Favored : 92.82 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.91 (0.17), residues: 2297 helix: -0.52 (0.25), residues: 405 sheet: -1.18 (0.21), residues: 617 loop : -1.54 (0.17), residues: 1275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 451 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 456 average time/residue: 0.3262 time to fit residues: 222.3446 Evaluate side-chains 310 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 209 optimal weight: 0.5980 chunk 222 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN B 539 GLN ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 GLN F 614 GLN F 617 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 89 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 18841 Z= 0.177 Angle : 0.674 8.547 25570 Z= 0.359 Chirality : 0.046 0.206 2814 Planarity : 0.005 0.070 3281 Dihedral : 6.189 34.809 2530 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.81 (0.17), residues: 2297 helix: -0.46 (0.25), residues: 405 sheet: -1.10 (0.21), residues: 607 loop : -1.48 (0.17), residues: 1285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 425 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 427 average time/residue: 0.3347 time to fit residues: 213.3075 Evaluate side-chains 290 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.462 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 199 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 614 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 18841 Z= 0.243 Angle : 0.705 7.992 25570 Z= 0.376 Chirality : 0.045 0.172 2814 Planarity : 0.005 0.072 3281 Dihedral : 6.265 33.425 2530 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.88 (0.17), residues: 2297 helix: -0.46 (0.24), residues: 411 sheet: -1.13 (0.21), residues: 612 loop : -1.57 (0.17), residues: 1274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 382 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 385 average time/residue: 0.3201 time to fit residues: 185.0270 Evaluate side-chains 277 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2074 time to fit residues: 3.3982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 20.0000 chunk 200 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 184 optimal weight: 0.0870 chunk 103 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 18841 Z= 0.184 Angle : 0.685 8.015 25570 Z= 0.364 Chirality : 0.047 0.254 2814 Planarity : 0.005 0.080 3281 Dihedral : 6.013 34.262 2530 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.92 % Favored : 92.95 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.80 (0.17), residues: 2297 helix: -0.27 (0.25), residues: 397 sheet: -0.96 (0.21), residues: 597 loop : -1.62 (0.17), residues: 1303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 391 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 395 average time/residue: 0.3186 time to fit residues: 190.1495 Evaluate side-chains 292 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 290 time to evaluate : 2.192 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1964 time to fit residues: 3.4715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 135 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 ASN ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 18841 Z= 0.229 Angle : 0.706 9.016 25570 Z= 0.376 Chirality : 0.047 0.401 2814 Planarity : 0.005 0.083 3281 Dihedral : 6.075 33.926 2530 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.71 % Favored : 92.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.84 (0.17), residues: 2297 helix: -0.30 (0.25), residues: 399 sheet: -1.01 (0.21), residues: 592 loop : -1.63 (0.17), residues: 1306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3138 time to fit residues: 174.0861 Evaluate side-chains 278 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 298 HIS ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 ASN ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 18841 Z= 0.280 Angle : 0.756 11.266 25570 Z= 0.407 Chirality : 0.047 0.221 2814 Planarity : 0.005 0.087 3281 Dihedral : 6.422 33.172 2530 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.62 % Favored : 91.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.93 (0.17), residues: 2297 helix: -0.55 (0.24), residues: 390 sheet: -1.07 (0.21), residues: 588 loop : -1.63 (0.17), residues: 1319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.3120 time to fit residues: 169.0723 Evaluate side-chains 270 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 193 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 89 optimal weight: 0.0570 chunk 162 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.7890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 18841 Z= 0.214 Angle : 0.715 9.827 25570 Z= 0.382 Chirality : 0.047 0.204 2814 Planarity : 0.005 0.089 3281 Dihedral : 6.173 33.134 2530 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.18 % Favored : 91.68 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.88 (0.17), residues: 2297 helix: -0.60 (0.25), residues: 388 sheet: -0.92 (0.21), residues: 576 loop : -1.62 (0.17), residues: 1333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.3027 time to fit residues: 168.2970 Evaluate side-chains 266 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.405 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 4.9990 chunk 218 optimal weight: 0.0470 chunk 133 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.8123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 18841 Z= 0.194 Angle : 0.727 9.870 25570 Z= 0.384 Chirality : 0.048 0.241 2814 Planarity : 0.005 0.093 3281 Dihedral : 6.022 33.446 2530 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.84 % Favored : 92.03 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.97 (0.17), residues: 2297 helix: -0.89 (0.25), residues: 397 sheet: -0.88 (0.21), residues: 576 loop : -1.65 (0.17), residues: 1324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 364 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 366 average time/residue: 0.2988 time to fit residues: 168.7243 Evaluate side-chains 262 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 2.238 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2190 time to fit residues: 3.4894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 168 optimal weight: 0.0970 chunk 26 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 344 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.042727 restraints weight = 145676.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.044296 restraints weight = 93591.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.045482 restraints weight = 66951.481| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.8390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 18841 Z= 0.258 Angle : 0.747 9.112 25570 Z= 0.400 Chirality : 0.047 0.199 2814 Planarity : 0.005 0.089 3281 Dihedral : 6.185 32.487 2530 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.23 % Favored : 90.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.99 (0.17), residues: 2297 helix: -1.03 (0.24), residues: 406 sheet: -0.90 (0.21), residues: 576 loop : -1.62 (0.17), residues: 1315 =============================================================================== Job complete usr+sys time: 4133.70 seconds wall clock time: 76 minutes 12.07 seconds (4572.07 seconds total)