Starting phenix.real_space_refine on Sun Jul 21 16:56:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2e_40981/07_2024/8t2e_40981.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2e_40981/07_2024/8t2e_40981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2e_40981/07_2024/8t2e_40981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2e_40981/07_2024/8t2e_40981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2e_40981/07_2024/8t2e_40981.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2e_40981/07_2024/8t2e_40981.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 102 5.16 5 C 9386 2.51 5 N 2574 2.21 5 O 2959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15021 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3392 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 5 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1009 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 946 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "E" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3333 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 401} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 946 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3344 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 7 Chain: "H" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 650 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'TRANS': 129} Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 130 Planarities with less than four sites: {'UNK:plan-1': 130} Unresolved non-hydrogen planarities: 130 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 8.85, per 1000 atoms: 0.59 Number of scatterers: 15021 At special positions: 0 Unit cell: (132.999, 132.999, 117.534, 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 102 16.00 O 2959 8.00 N 2574 7.00 C 9386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.09 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.23 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.09 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.01 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.02 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.06 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.10 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 197 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 241 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 289 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 355 " " NAG A 611 " - " ASN A 363 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 448 " " NAG A 614 " - " ASN A 392 " " NAG A 615 " - " ASN A 295 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 241 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 332 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 295 " " NAG E 612 " - " ASN E 386 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 160 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 234 " " NAG F 605 " - " ASN F 241 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 289 " " NAG F 608 " - " ASN F 295 " " NAG F 609 " - " ASN F 301 " " NAG F 610 " - " ASN F 332 " " NAG F 611 " - " ASN F 339 " " NAG F 612 " - " ASN F 355 " " NAG F 613 " - " ASN F 363 " " NAG F 614 " - " ASN F 386 " " NAG F 615 " - " ASN F 448 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN E 156 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN F 262 " Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 2.3 seconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3532 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 27 sheets defined 26.7% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.043A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.669A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 522 through 528 removed outlier: 4.480A pdb=" N ALA C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 572 through 596 Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 662 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.921A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.206A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.604A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.212A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 537 No H-bonds generated for 'chain 'D' and resid 535 through 537' Processing helix chain 'D' and resid 573 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'F' and resid 67 through 73 Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.026A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 475 through 484 removed outlier: 4.008A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 5.366A pdb=" N UNK H 66 " --> pdb=" O UNK H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'L' and resid 91 through 93 No H-bonds generated for 'chain 'L' and resid 91 through 93' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.351A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.861A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.672A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.144A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 302 removed outlier: 6.688A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 334 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 469 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.458A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.117A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.639A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.933A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 removed outlier: 4.396A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 413 through 421 current: chain 'E' and resid 465 through 470 Processing sheet with id=AB7, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.262A pdb=" N CYS D 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N TYR F 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR D 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL F 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL D 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.558A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.495A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 283 through 302 removed outlier: 6.738A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 329 through 334 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 466 through 470 Processing sheet with id=AC5, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.570A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AC7, first strand: chain 'H' and resid 34 through 41 removed outlier: 5.995A pdb=" N UNK H 39 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N UNK H 47 " --> pdb=" O UNK H 39 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N UNK H 41 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N UNK H 45 " --> pdb=" O UNK H 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 117 through 120 Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'L' and resid 32 through 36 removed outlier: 6.778A pdb=" N UNK L 33 " --> pdb=" O UNK L 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 51 through 52 current: chain 'L' and resid 94 through 97 476 hydrogen bonds defined for protein. 1308 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: 4.57 Time building geometry restraints manager: 6.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4294 1.33 - 1.48: 4621 1.48 - 1.63: 6211 1.63 - 1.78: 52 1.78 - 1.93: 91 Bond restraints: 15269 Sorted by residual: bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.509 -0.111 1.60e-02 3.91e+03 4.84e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.79e+01 bond pdb=" NE ARG E 504 " pdb=" CZ ARG E 504 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.49e+01 bond pdb=" CB ILE F 184 " pdb=" CG1 ILE F 184 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" NE ARG F 456 " pdb=" CZ ARG F 456 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.06e+01 ... (remaining 15264 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.10: 408 106.10 - 113.14: 8291 113.14 - 120.17: 6000 120.17 - 127.21: 5841 127.21 - 134.25: 210 Bond angle restraints: 20750 Sorted by residual: angle pdb=" N GLU E 87 " pdb=" CA GLU E 87 " pdb=" C GLU E 87 " ideal model delta sigma weight residual 111.28 120.05 -8.77 1.09e+00 8.42e-01 6.47e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.58 -8.02 1.01e+00 9.80e-01 6.30e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.01e+00 9.80e-01 5.92e+01 angle pdb=" C ALA A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta sigma weight residual 120.31 127.53 -7.22 9.80e-01 1.04e+00 5.43e+01 angle pdb=" N TRP F 395 " pdb=" CA TRP F 395 " pdb=" C TRP F 395 " ideal model delta sigma weight residual 113.17 122.41 -9.24 1.26e+00 6.30e-01 5.37e+01 ... (remaining 20745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.01: 9725 21.01 - 42.03: 212 42.03 - 63.04: 59 63.04 - 84.06: 29 84.06 - 105.07: 17 Dihedral angle restraints: 10042 sinusoidal: 4637 harmonic: 5405 Sorted by residual: dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 39.05 53.95 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS F 378 " pdb=" SG CYS F 378 " pdb=" SG CYS F 445 " pdb=" CB CYS F 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.79 42.79 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -127.32 41.32 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 10039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1821 0.111 - 0.222: 467 0.222 - 0.333: 184 0.333 - 0.445: 103 0.445 - 0.556: 20 Chirality restraints: 2595 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.20e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.26e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.96e+01 ... (remaining 2592 not shown) Planarity restraints: 2615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 339 " 0.083 2.00e-02 2.50e+03 8.66e-02 9.38e+01 pdb=" CG ASN E 339 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN E 339 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 339 " -0.135 2.00e-02 2.50e+03 pdb=" C1 NAG E 609 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " -0.071 2.00e-02 2.50e+03 7.44e-02 6.92e+01 pdb=" CG ASN A 392 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " 0.115 2.00e-02 2.50e+03 pdb=" C1 NAG A 614 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 160 " 0.066 2.00e-02 2.50e+03 6.86e-02 5.88e+01 pdb=" CG ASN F 160 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN F 160 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN F 160 " -0.106 2.00e-02 2.50e+03 pdb=" C1 NAG F 602 " 0.084 2.00e-02 2.50e+03 ... (remaining 2612 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 5330 2.88 - 3.38: 13209 3.38 - 3.89: 24306 3.89 - 4.39: 27879 4.39 - 4.90: 45093 Nonbonded interactions: 115817 Sorted by model distance: nonbonded pdb=" OG SER E 334 " pdb=" OG1 THR E 337 " model vdw 2.373 2.440 nonbonded pdb=" O THR F 248 " pdb=" CB THR F 248 " model vdw 2.375 2.776 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.416 2.496 nonbonded pdb=" NZ LYS D 574 " pdb=" OD1 ASP F 107 " model vdw 2.430 2.520 nonbonded pdb=" N THR E 240 " pdb=" O THR E 240 " model vdw 2.443 2.496 ... (remaining 115812 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 34 through 57 or resid 66 through 77 or resid 83 through 1 \ 40 or resid 150 through 163 or resid 165 through 206 or (resid 207 and (name N o \ r name CA or name C or name O or name CB )) or resid 208 through 355 or resid 35 \ 7 through 364 or resid 370 through 395 or resid 412 through 456 or resid 465 thr \ ough 504 or resid 601 through 612)) selection = (chain 'E' and (resid 34 through 77 or resid 83 through 140 or resid 150 through \ 182 or resid 189 through 364 or resid 370 through 456 or resid 465 through 504 \ or resid 601 through 612)) selection = (chain 'F' and (resid 34 through 57 or resid 66 through 163 or resid 165 through \ 182 or resid 189 through 206 or (resid 207 and (name N or name CA or name C or \ name O or name CB )) or resid 208 through 355 or resid 357 through 364 or resid \ 370 through 395 or resid 412 through 456 or resid 465 through 504 or resid 601 t \ hrough 612)) } ncs_group { reference = (chain 'B' and (resid 522 through 663 or resid 701 through 702)) selection = chain 'C' selection = (chain 'D' and (resid 522 through 663 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' } 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 41.330 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.080 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.023 0.202 15269 Z= 1.420 Angle : 1.668 13.300 20750 Z= 1.074 Chirality : 0.140 0.556 2595 Planarity : 0.009 0.048 2559 Dihedral : 11.270 105.070 6411 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.78 % Favored : 98.09 % Rotamer: Outliers : 0.14 % Allowed : 0.82 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1574 helix: -0.28 (0.24), residues: 425 sheet: 1.04 (0.24), residues: 383 loop : 0.77 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.010 TRP A 479 HIS 0.006 0.002 HIS A 216 PHE 0.028 0.006 PHE F 383 TYR 0.034 0.006 TYR E 191 ARG 0.007 0.001 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 479 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7692 (m-90) cc_final: 0.7299 (m-90) REVERT: A 100 MET cc_start: 0.9169 (mtp) cc_final: 0.8760 (mtp) REVERT: A 150 MET cc_start: 0.8320 (mmm) cc_final: 0.7961 (tpp) REVERT: A 192 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7071 (mtt90) REVERT: A 289 ASN cc_start: 0.8068 (t0) cc_final: 0.7820 (t0) REVERT: B 635 ILE cc_start: 0.8919 (mm) cc_final: 0.8663 (tt) REVERT: C 626 MET cc_start: 0.8128 (ttm) cc_final: 0.7909 (ttm) REVERT: E 39 TYR cc_start: 0.8895 (m-80) cc_final: 0.8676 (m-80) REVERT: E 275 GLU cc_start: 0.7944 (tt0) cc_final: 0.7598 (tt0) REVERT: E 297 THR cc_start: 0.8172 (m) cc_final: 0.7895 (p) REVERT: E 500 ARG cc_start: 0.4442 (mtm180) cc_final: 0.3728 (ptt90) REVERT: F 103 GLN cc_start: 0.8684 (tt0) cc_final: 0.8476 (tt0) REVERT: F 207 LYS cc_start: 0.8636 (pttt) cc_final: 0.8260 (mmtp) REVERT: F 231 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8491 (mmmt) REVERT: F 248 THR cc_start: 0.8649 (p) cc_final: 0.8437 (p) REVERT: F 264 SER cc_start: 0.8368 (m) cc_final: 0.7858 (m) REVERT: F 482 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7650 (mm-30) outliers start: 2 outliers final: 1 residues processed: 480 average time/residue: 0.2984 time to fit residues: 200.6178 Evaluate side-chains 313 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 197 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 348 GLN A 352 HIS A 356 ASN A 422 GLN B 630 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN F 105 HIS F 170 GLN F 203 GLN F 283 ASN F 348 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15269 Z= 0.243 Angle : 0.633 7.142 20750 Z= 0.326 Chirality : 0.047 0.293 2595 Planarity : 0.004 0.037 2559 Dihedral : 8.055 73.213 3312 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.46 % Favored : 98.48 % Rotamer: Outliers : 2.40 % Allowed : 9.96 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1574 helix: 1.49 (0.28), residues: 390 sheet: 0.90 (0.23), residues: 436 loop : 0.35 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 479 HIS 0.004 0.001 HIS A 352 PHE 0.020 0.002 PHE E 468 TYR 0.022 0.002 TYR E 486 ARG 0.006 0.001 ARG F 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 340 time to evaluate : 1.584 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: A 78 ASP cc_start: 0.7518 (m-30) cc_final: 0.7132 (m-30) REVERT: A 192 ARG cc_start: 0.7401 (mtm180) cc_final: 0.6938 (mtt90) REVERT: A 289 ASN cc_start: 0.8194 (t0) cc_final: 0.7954 (t0) REVERT: A 500 ARG cc_start: 0.7449 (mtt180) cc_final: 0.6848 (mtp-110) REVERT: E 443 ILE cc_start: 0.8679 (mt) cc_final: 0.8468 (mm) REVERT: F 150 MET cc_start: 0.7013 (ptp) cc_final: 0.6492 (ptt) REVERT: F 207 LYS cc_start: 0.8594 (pttt) cc_final: 0.8226 (mmtp) REVERT: F 363 ASN cc_start: 0.7673 (t0) cc_final: 0.7161 (p0) REVERT: F 475 MET cc_start: 0.8319 (tpp) cc_final: 0.8094 (mmt) outliers start: 35 outliers final: 21 residues processed: 352 average time/residue: 0.2828 time to fit residues: 144.1432 Evaluate side-chains 317 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 296 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 113 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 133 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 258 GLN A 356 ASN E 195 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15269 Z= 0.197 Angle : 0.542 7.947 20750 Z= 0.279 Chirality : 0.044 0.301 2595 Planarity : 0.003 0.033 2559 Dihedral : 6.433 50.063 3312 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.95 % Allowed : 11.68 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1574 helix: 1.67 (0.28), residues: 390 sheet: 0.97 (0.24), residues: 418 loop : 0.16 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 479 HIS 0.003 0.001 HIS E 374 PHE 0.017 0.002 PHE E 53 TYR 0.020 0.002 TYR E 486 ARG 0.007 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 318 time to evaluate : 1.546 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: A 78 ASP cc_start: 0.7432 (m-30) cc_final: 0.7230 (m-30) REVERT: A 192 ARG cc_start: 0.7516 (mtm180) cc_final: 0.7038 (mtt90) REVERT: A 469 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7521 (mmt90) REVERT: A 500 ARG cc_start: 0.7553 (mtt180) cc_final: 0.6946 (mtp-110) REVERT: E 103 GLN cc_start: 0.8733 (tp40) cc_final: 0.8255 (tp40) REVERT: E 482 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7595 (mm-30) REVERT: E 484 TYR cc_start: 0.8920 (p90) cc_final: 0.8659 (p90) REVERT: F 150 MET cc_start: 0.7114 (ptp) cc_final: 0.6620 (ptt) REVERT: F 160 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8150 (m110) REVERT: F 207 LYS cc_start: 0.8571 (pttt) cc_final: 0.8111 (mppt) outliers start: 43 outliers final: 30 residues processed: 338 average time/residue: 0.2623 time to fit residues: 129.6976 Evaluate side-chains 319 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 288 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 375 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN C 630 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15269 Z= 0.266 Angle : 0.559 8.523 20750 Z= 0.285 Chirality : 0.045 0.308 2595 Planarity : 0.003 0.031 2559 Dihedral : 5.851 48.804 3312 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.43 % Allowed : 13.19 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1574 helix: 1.53 (0.28), residues: 397 sheet: 0.85 (0.24), residues: 419 loop : -0.07 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.003 0.001 HIS E 105 PHE 0.015 0.002 PHE E 53 TYR 0.021 0.002 TYR E 173 ARG 0.006 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 305 time to evaluate : 1.667 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: A 96 TRP cc_start: 0.7885 (m-90) cc_final: 0.7484 (m-90) REVERT: A 192 ARG cc_start: 0.7626 (mtm180) cc_final: 0.7138 (mtt90) REVERT: A 363 ASN cc_start: 0.7960 (p0) cc_final: 0.7672 (p0) REVERT: A 469 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.7639 (mmt90) REVERT: A 500 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7146 (mtp-110) REVERT: E 482 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7534 (mm-30) REVERT: D 634 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7928 (mm-30) REVERT: F 160 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8154 (m110) REVERT: F 180 ASP cc_start: 0.6918 (m-30) cc_final: 0.6610 (m-30) REVERT: F 207 LYS cc_start: 0.8625 (pttt) cc_final: 0.8089 (mppt) REVERT: F 264 SER cc_start: 0.8721 (m) cc_final: 0.8513 (m) REVERT: F 363 ASN cc_start: 0.7733 (t0) cc_final: 0.7257 (p0) outliers start: 50 outliers final: 39 residues processed: 329 average time/residue: 0.2561 time to fit residues: 123.7885 Evaluate side-chains 326 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 286 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 0.0670 chunk 131 optimal weight: 0.0040 chunk 72 optimal weight: 0.4980 chunk 150 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 158 optimal weight: 0.0170 chunk 44 optimal weight: 2.9990 overall best weight: 0.2568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15269 Z= 0.115 Angle : 0.462 7.590 20750 Z= 0.238 Chirality : 0.042 0.263 2595 Planarity : 0.003 0.035 2559 Dihedral : 5.076 40.539 3312 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.72 % Allowed : 15.18 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1574 helix: 1.95 (0.28), residues: 385 sheet: 0.82 (0.24), residues: 427 loop : 0.05 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 479 HIS 0.002 0.000 HIS E 374 PHE 0.015 0.001 PHE E 53 TYR 0.019 0.001 TYR A 173 ARG 0.007 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 318 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7699 (m-90) cc_final: 0.7174 (m-90) REVERT: A 153 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6971 (tm-30) REVERT: A 192 ARG cc_start: 0.7506 (mtm180) cc_final: 0.7223 (mtm180) REVERT: A 469 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.7609 (mmt90) REVERT: A 484 TYR cc_start: 0.8965 (p90) cc_final: 0.8324 (p90) REVERT: A 500 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7261 (mtp-110) REVERT: B 616 ASN cc_start: 0.6515 (p0) cc_final: 0.6278 (p0) REVERT: E 150 MET cc_start: 0.6872 (mmm) cc_final: 0.6541 (tpp) REVERT: E 178 ARG cc_start: 0.7327 (ptm-80) cc_final: 0.7100 (ptm-80) REVERT: D 596 TRP cc_start: 0.8883 (m-10) cc_final: 0.8525 (m-10) REVERT: F 150 MET cc_start: 0.7052 (ptp) cc_final: 0.6483 (ptt) REVERT: F 160 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8121 (m110) REVERT: F 180 ASP cc_start: 0.6765 (m-30) cc_final: 0.6420 (m-30) REVERT: F 207 LYS cc_start: 0.8611 (pttt) cc_final: 0.8096 (mppt) REVERT: F 264 SER cc_start: 0.8674 (m) cc_final: 0.8473 (m) REVERT: F 363 ASN cc_start: 0.7610 (t0) cc_final: 0.7076 (p0) outliers start: 25 outliers final: 16 residues processed: 329 average time/residue: 0.2675 time to fit residues: 129.0261 Evaluate side-chains 318 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 301 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 375 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15269 Z= 0.165 Angle : 0.490 8.496 20750 Z= 0.249 Chirality : 0.043 0.273 2595 Planarity : 0.003 0.032 2559 Dihedral : 4.894 38.077 3310 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.40 % Allowed : 15.80 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1574 helix: 2.11 (0.28), residues: 380 sheet: 0.87 (0.24), residues: 415 loop : -0.07 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 479 HIS 0.002 0.000 HIS E 374 PHE 0.015 0.001 PHE E 53 TYR 0.025 0.001 TYR A 173 ARG 0.007 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 313 time to evaluate : 1.555 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: A 57 ASP cc_start: 0.7670 (m-30) cc_final: 0.7430 (m-30) REVERT: A 78 ASP cc_start: 0.7680 (m-30) cc_final: 0.7459 (m-30) REVERT: A 96 TRP cc_start: 0.7636 (m-90) cc_final: 0.7251 (m-90) REVERT: A 153 GLU cc_start: 0.7288 (tm-30) cc_final: 0.7003 (tm-30) REVERT: A 192 ARG cc_start: 0.7479 (mtm180) cc_final: 0.7181 (mtm180) REVERT: A 484 TYR cc_start: 0.8949 (p90) cc_final: 0.8346 (p90) REVERT: A 500 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7302 (mtp-110) REVERT: C 530 MET cc_start: 0.8928 (mtt) cc_final: 0.8719 (mtm) REVERT: D 596 TRP cc_start: 0.8917 (m-10) cc_final: 0.8605 (m-10) REVERT: F 160 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8045 (m110) REVERT: F 180 ASP cc_start: 0.6862 (m-30) cc_final: 0.6556 (m-30) REVERT: F 207 LYS cc_start: 0.8632 (pttt) cc_final: 0.8104 (mppt) REVERT: F 264 SER cc_start: 0.8652 (m) cc_final: 0.8441 (m) REVERT: F 363 ASN cc_start: 0.7622 (t0) cc_final: 0.7092 (p0) outliers start: 35 outliers final: 22 residues processed: 330 average time/residue: 0.2617 time to fit residues: 127.4172 Evaluate side-chains 319 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 296 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 426 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15269 Z= 0.332 Angle : 0.593 8.583 20750 Z= 0.296 Chirality : 0.046 0.265 2595 Planarity : 0.003 0.026 2559 Dihedral : 5.583 46.270 3310 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.37 % Allowed : 15.66 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1574 helix: 1.66 (0.28), residues: 392 sheet: 0.69 (0.25), residues: 403 loop : -0.40 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.003 0.001 HIS E 105 PHE 0.014 0.002 PHE B 522 TYR 0.025 0.002 TYR A 173 ARG 0.006 0.001 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 293 time to evaluate : 1.556 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: A 92 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 96 TRP cc_start: 0.7737 (m-90) cc_final: 0.7340 (m-90) REVERT: A 153 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7132 (tm-30) REVERT: A 192 ARG cc_start: 0.7639 (mtm180) cc_final: 0.7249 (mtt90) REVERT: A 500 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7379 (mtp-110) REVERT: C 530 MET cc_start: 0.9003 (mtt) cc_final: 0.8759 (mtm) REVERT: E 100 MET cc_start: 0.8924 (mtp) cc_final: 0.8616 (mtm) REVERT: E 482 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7532 (mm-30) REVERT: F 160 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7946 (m110) REVERT: F 180 ASP cc_start: 0.6992 (m-30) cc_final: 0.6788 (m-30) REVERT: F 207 LYS cc_start: 0.8586 (pttt) cc_final: 0.8045 (mppt) REVERT: F 363 ASN cc_start: 0.7839 (t0) cc_final: 0.7353 (p0) outliers start: 49 outliers final: 39 residues processed: 314 average time/residue: 0.2573 time to fit residues: 118.6476 Evaluate side-chains 324 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 284 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 370 GLU Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 0.0270 chunk 138 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15269 Z= 0.160 Angle : 0.501 9.457 20750 Z= 0.254 Chirality : 0.043 0.240 2595 Planarity : 0.003 0.037 2559 Dihedral : 5.252 44.162 3310 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.40 % Allowed : 17.45 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1574 helix: 1.81 (0.28), residues: 392 sheet: 0.65 (0.24), residues: 416 loop : -0.37 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 35 HIS 0.002 0.000 HIS E 374 PHE 0.016 0.001 PHE E 53 TYR 0.024 0.001 TYR A 173 ARG 0.008 0.000 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 299 time to evaluate : 1.405 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: A 96 TRP cc_start: 0.7627 (m-90) cc_final: 0.7214 (m-90) REVERT: A 153 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7069 (tm-30) REVERT: A 192 ARG cc_start: 0.7611 (mtm180) cc_final: 0.7254 (mtt90) REVERT: A 500 ARG cc_start: 0.7754 (mtt180) cc_final: 0.7401 (mtp-110) REVERT: C 530 MET cc_start: 0.9009 (mtt) cc_final: 0.8738 (mtm) REVERT: E 100 MET cc_start: 0.8891 (mtp) cc_final: 0.8576 (mtm) REVERT: E 358 ILE cc_start: 0.6931 (mt) cc_final: 0.6430 (mm) REVERT: E 482 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7431 (mm-30) REVERT: D 596 TRP cc_start: 0.8963 (m-10) cc_final: 0.8730 (m-10) REVERT: F 160 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7938 (m110) REVERT: F 180 ASP cc_start: 0.6982 (m-30) cc_final: 0.6773 (m-30) REVERT: F 207 LYS cc_start: 0.8525 (pttt) cc_final: 0.8033 (mppt) REVERT: F 363 ASN cc_start: 0.7740 (t0) cc_final: 0.7223 (p0) outliers start: 35 outliers final: 30 residues processed: 317 average time/residue: 0.2615 time to fit residues: 121.6639 Evaluate side-chains 319 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 288 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15269 Z= 0.308 Angle : 0.577 14.303 20750 Z= 0.286 Chirality : 0.045 0.251 2595 Planarity : 0.003 0.038 2559 Dihedral : 5.564 46.605 3310 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.23 % Allowed : 16.69 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1574 helix: 1.60 (0.28), residues: 393 sheet: 0.57 (0.25), residues: 394 loop : -0.52 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 316 HIS 0.002 0.001 HIS F 72 PHE 0.016 0.002 PHE E 53 TYR 0.023 0.002 TYR A 173 ARG 0.009 0.001 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 285 time to evaluate : 1.672 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: A 96 TRP cc_start: 0.7737 (m-90) cc_final: 0.7325 (m-90) REVERT: A 153 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7136 (tm-30) REVERT: A 192 ARG cc_start: 0.7579 (mtm180) cc_final: 0.7251 (mtt90) REVERT: A 432 GLN cc_start: 0.7895 (mp10) cc_final: 0.7615 (mp10) REVERT: A 500 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7440 (mtp-110) REVERT: B 595 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8636 (tt) REVERT: C 530 MET cc_start: 0.9004 (mtt) cc_final: 0.8793 (mtm) REVERT: E 100 MET cc_start: 0.8955 (mtp) cc_final: 0.8676 (mtm) REVERT: E 358 ILE cc_start: 0.6969 (mt) cc_final: 0.6435 (mm) REVERT: E 482 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7524 (mm-30) REVERT: F 160 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7903 (m110) REVERT: F 180 ASP cc_start: 0.7080 (m-30) cc_final: 0.6815 (m-30) REVERT: F 207 LYS cc_start: 0.8533 (pttt) cc_final: 0.8039 (mppt) REVERT: F 363 ASN cc_start: 0.7804 (t0) cc_final: 0.7296 (p0) outliers start: 47 outliers final: 35 residues processed: 308 average time/residue: 0.2612 time to fit residues: 119.0476 Evaluate side-chains 314 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 277 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 15269 Z= 0.411 Angle : 0.659 13.051 20750 Z= 0.326 Chirality : 0.048 0.284 2595 Planarity : 0.004 0.034 2559 Dihedral : 6.225 50.825 3310 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.82 % Allowed : 17.17 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1574 helix: 1.36 (0.27), residues: 393 sheet: 0.28 (0.25), residues: 412 loop : -0.72 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 316 HIS 0.003 0.001 HIS F 72 PHE 0.017 0.002 PHE E 53 TYR 0.023 0.002 TYR A 173 ARG 0.008 0.001 ARG A 469 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 284 time to evaluate : 1.510 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: A 96 TRP cc_start: 0.7896 (m-90) cc_final: 0.7524 (m-90) REVERT: A 153 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 192 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7254 (mtt90) REVERT: A 432 GLN cc_start: 0.7975 (mp10) cc_final: 0.7541 (mp10) REVERT: A 500 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7340 (mtm110) REVERT: B 595 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8714 (tt) REVERT: B 640 GLN cc_start: 0.8039 (mp10) cc_final: 0.7823 (mp10) REVERT: E 100 MET cc_start: 0.9019 (mtp) cc_final: 0.8774 (mtm) REVERT: E 178 ARG cc_start: 0.7517 (ptm-80) cc_final: 0.7283 (ptm-80) REVERT: E 358 ILE cc_start: 0.7060 (mt) cc_final: 0.6418 (mm) REVERT: E 482 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7600 (mm-30) REVERT: F 160 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7868 (m110) REVERT: F 180 ASP cc_start: 0.7145 (m-30) cc_final: 0.6918 (m-30) REVERT: F 207 LYS cc_start: 0.8497 (pttt) cc_final: 0.8038 (mppt) REVERT: F 363 ASN cc_start: 0.7877 (t0) cc_final: 0.7502 (p0) outliers start: 41 outliers final: 39 residues processed: 308 average time/residue: 0.2659 time to fit residues: 119.1236 Evaluate side-chains 320 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 279 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN E 103 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.158211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.136364 restraints weight = 20321.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.140325 restraints weight = 10449.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.142814 restraints weight = 6843.918| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15269 Z= 0.166 Angle : 0.531 15.674 20750 Z= 0.265 Chirality : 0.043 0.248 2595 Planarity : 0.003 0.033 2559 Dihedral : 5.560 46.001 3310 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.54 % Allowed : 17.38 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1574 helix: 1.72 (0.28), residues: 393 sheet: 0.36 (0.25), residues: 424 loop : -0.60 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 316 HIS 0.002 0.000 HIS E 374 PHE 0.016 0.001 PHE E 53 TYR 0.026 0.001 TYR A 173 ARG 0.008 0.001 ARG A 469 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3189.42 seconds wall clock time: 57 minutes 55.60 seconds (3475.60 seconds total)