Starting phenix.real_space_refine on Thu Jul 25 00:29:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2f_40982/07_2024/8t2f_40982_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2f_40982/07_2024/8t2f_40982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2f_40982/07_2024/8t2f_40982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2f_40982/07_2024/8t2f_40982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2f_40982/07_2024/8t2f_40982_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2f_40982/07_2024/8t2f_40982_trim.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 8826 2.51 5 N 2412 2.21 5 O 2761 1.98 5 H 12013 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 26110 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 6678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6678 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1751 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1620 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 1 Chain: "E" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 5807 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 20, 'TRANS': 347} Chain breaks: 10 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1828 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "F" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6546 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain breaks: 7 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 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: 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: "J" 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: "K" 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: "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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" 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: "F" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 12.85, per 1000 atoms: 0.49 Number of scatterers: 26110 At special positions: 0 Unit cell: (149.495, 122.689, 116.503, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 2761 8.00 N 2412 7.00 C 8826 6.00 H 12013 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.10 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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=2.09 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 E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.13 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.11 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.05 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.14 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 149 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 152 " " 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 363 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 295 " " NAG A 611 " - " ASN A 355 " " NAG A 612 " - " ASN A 392 " " NAG A 613 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 152 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 276 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 332 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 386 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 152 " " NAG F 603 " - " ASN F 148 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 241 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 289 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 332 " " NAG F 611 " - " ASN F 355 " " NAG F 612 " - " ASN F 363 " " NAG F 613 " - " ASN F 386 " " NAG F 614 " - " ASN F 448 " " NAG F 615 " - " ASN F 133 " " NAG F 616 " - " ASN F 301 " " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN F 262 " Time building additional restraints: 20.76 Conformation dependent library (CDL) restraints added in 2.6 seconds 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3334 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 24.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.088A 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 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.796A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 removed outlier: 3.881A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 594 removed outlier: 3.760A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 Processing helix chain 'C' and resid 532 through 535 removed outlier: 4.234A pdb=" N MET C 535 " --> pdb=" O ALA C 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 535' Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 611 through 615 Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 639 through 649 Processing helix chain 'E' and resid 98 through 115 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.528A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 346 Processing helix chain 'E' and resid 348 through 352 Processing helix chain 'E' and resid 474 through 481 Processing helix chain 'D' and resid 531 through 536 removed outlier: 4.075A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 660 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 98 through 117 removed outlier: 3.514A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 169 through 171 No H-bonds generated for 'chain 'F' and resid 169 through 171' Processing helix chain 'F' and resid 334 through 350 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 480 Processing helix chain 'F' and resid 481 through 484 removed outlier: 4.288A pdb=" N TYR F 484 " --> pdb=" O SER F 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'H' and resid 62 through 65 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 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.596A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 162 through 169 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.556A 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 283 through 312 removed outlier: 6.613A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A 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 467 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 603 through 604 Processing sheet with id=AA9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'E' and resid 130 through 132 Processing sheet with id=AB4, first strand: chain 'E' and resid 173 through 174 Processing sheet with id=AB5, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.263A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.717A 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 297 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 330 through 333 current: chain 'E' and resid 469 through 470 Processing sheet with id=AB7, first strand: chain 'E' and resid 305 through 312 removed outlier: 6.643A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 603 through 609 removed outlier: 4.820A pdb=" N VAL F 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'F' and resid 163 through 168 Processing sheet with id=AC4, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.733A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC5, 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 284 through 302 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 330 through 333 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=AC6, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.432A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.923A pdb=" N UNK H 16 " --> pdb=" O UNK H 85 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC9, first strand: chain 'H' and resid 58 through 60 removed outlier: 7.059A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AD3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.586A pdb=" N UNK L 53 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1152 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: 9.16 Time building geometry restraints manager: 21.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 12009 1.05 - 1.27: 2274 1.27 - 1.48: 6032 1.48 - 1.70: 5904 1.70 - 1.91: 130 Bond restraints: 26349 Sorted by residual: bond pdb=" NE ARG F 504 " pdb=" CZ ARG F 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.71e+01 bond pdb=" CD2 TRP B 571 " pdb=" CE3 TRP B 571 " ideal model delta sigma weight residual 1.398 1.507 -0.109 1.60e-02 3.91e+03 4.65e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.57e+01 bond pdb=" CZ2 TRP B 571 " pdb=" CH2 TRP B 571 " ideal model delta sigma weight residual 1.368 1.492 -0.124 1.90e-02 2.77e+03 4.25e+01 bond pdb=" CB ILE F 176 " pdb=" CG1 ILE F 176 " ideal model delta sigma weight residual 1.530 1.660 -0.130 2.00e-02 2.50e+03 4.20e+01 ... (remaining 26344 not shown) Histogram of bond angle deviations from ideal: 94.86 - 102.79: 162 102.79 - 110.71: 25415 110.71 - 118.64: 9657 118.64 - 126.56: 11224 126.56 - 134.49: 290 Bond angle restraints: 46748 Sorted by residual: angle pdb=" N CYS A 196 " pdb=" CA CYS A 196 " pdb=" C CYS A 196 " ideal model delta sigma weight residual 114.12 101.61 12.51 1.39e+00 5.18e-01 8.11e+01 angle pdb=" N ILE E 424 " pdb=" CA ILE E 424 " pdb=" C ILE E 424 " ideal model delta sigma weight residual 107.80 119.93 -12.13 1.45e+00 4.76e-01 6.99e+01 angle pdb=" N SER A 115 " pdb=" CA SER A 115 " pdb=" C SER A 115 " ideal model delta sigma weight residual 110.53 99.88 10.65 1.29e+00 6.01e-01 6.82e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.02e+00 9.61e-01 6.73e+01 angle pdb=" N PHE E 383 " pdb=" CA PHE E 383 " pdb=" C PHE E 383 " ideal model delta sigma weight residual 112.23 121.44 -9.21 1.26e+00 6.30e-01 5.34e+01 ... (remaining 46743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 12788 21.07 - 42.13: 350 42.13 - 63.20: 155 63.20 - 84.26: 32 84.26 - 105.33: 19 Dihedral angle restraints: 13344 sinusoidal: 7464 harmonic: 5880 Sorted by residual: dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 -177.73 -89.27 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS D 605 " pdb=" SG CYS D 605 " pdb=" SG CYS F 501 " pdb=" CB CYS F 501 " ideal model delta sinusoidal sigma weight residual -86.00 -44.26 -41.74 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -125.46 39.46 1 1.00e+01 1.00e-02 2.19e+01 ... (remaining 13341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1681 0.104 - 0.208: 451 0.208 - 0.311: 164 0.311 - 0.415: 83 0.415 - 0.519: 43 Chirality restraints: 2422 Sorted by residual: chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.31e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.06e+01 ... (remaining 2419 not shown) Planarity restraints: 3903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 295 " 0.116 2.00e-02 2.50e+03 9.03e-02 1.22e+02 pdb=" CG ASN E 295 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN E 295 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN E 295 " -0.094 2.00e-02 2.50e+03 pdb="HD21 ASN E 295 " -0.075 2.00e-02 2.50e+03 pdb=" C1 NAG E 608 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 301 " -0.105 2.00e-02 2.50e+03 8.30e-02 1.03e+02 pdb=" CG ASN F 301 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN F 301 " 0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN F 301 " 0.085 2.00e-02 2.50e+03 pdb="HD21 ASN F 301 " 0.062 2.00e-02 2.50e+03 pdb=" C1 NAG F 616 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " -0.105 2.00e-02 2.50e+03 8.07e-02 9.77e+01 pdb=" CG ASN A 339 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " 0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " 0.082 2.00e-02 2.50e+03 pdb="HD21 ASN A 339 " 0.060 2.00e-02 2.50e+03 pdb=" C1 NAG A 613 " -0.119 2.00e-02 2.50e+03 ... (remaining 3900 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 388 2.04 - 2.68: 36431 2.68 - 3.32: 70557 3.32 - 3.96: 92504 3.96 - 4.60: 143432 Nonbonded interactions: 343312 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" HG1 THR F 499 " model vdw 1.401 1.850 nonbonded pdb=" H CYS A 196 " pdb=" H ASN A 197 " model vdw 1.456 2.100 nonbonded pdb=" OG1 THR A 37 " pdb=" HG1 THR A 499 " model vdw 1.471 1.850 nonbonded pdb=" OE2 GLU F 290 " pdb=" HZ1 LYS F 344 " model vdw 1.666 1.850 nonbonded pdb=" HG1 THR A 37 " pdb=" HG1 THR A 499 " model vdw 1.751 2.100 ... (remaining 343307 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 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 134 through 153 or (resid 161 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3) \ ) or resid 162 through 288 or (resid 289 and (name N or name CA or name C or nam \ e O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name H \ B2 or name HB3 or name HD21)) or resid 290 through 300 or (resid 301 and (name N \ or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or \ name H or name HA or name HB2 or name HB3 or name HD21)) or resid 302 through 3 \ 21 or (resid 323 and (name N or name CA or name C or name O or name CB or name C \ G1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 or na \ me HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) or re \ sid 323A through 397 or resid 412 through 455 or (resid 464 and (name N or name \ CA or name C or name O or name CB or name OG1 or name CG2 or name HA or name HB \ or name HG1 or name HG21 or name HG22 or name HG23)) or resid 465 through 503 or \ resid 601 through 613)) selection = (chain 'F' and (resid 34 through 57 or (resid 67 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 68 through 338 or (resid 339 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 340 \ through 391 or (resid 392 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 \ or name HD21)) or resid 393 through 503 or resid 604 through 616)) } ncs_group { reference = (chain 'B' and ((resid 522 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 523 through 546 or (resid 572 and (name N or name CA or name C \ or name O or name HA2 or name HA3)) or resid 573 through 649 or resid 702)) selection = (chain 'C' and (resid 522 through 604 or (resid 605 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 606 through 610 or (resid 611 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name \ HB2 or name HB3 or name HD21)) or resid 612 through 649 or resid 701)) selection = (chain 'D' and (resid 522 through 546 or (resid 572 and (name N or name CA or na \ me C or name O or name HA2 or name HA3)) or resid 573 through 649 or resid 702)) \ } ncs_group { reference = chain 'G' selection = chain 'J' } ncs_group { reference = (chain 'H' and resid 12 through 116) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' } 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: 3.150 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: 0.400 Extract box with map and model: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 82.830 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.022 0.134 14336 Z= 1.347 Angle : 1.691 12.514 19484 Z= 1.099 Chirality : 0.137 0.519 2422 Planarity : 0.009 0.058 2403 Dihedral : 11.356 105.329 5914 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.22 % Allowed : 0.44 % Favored : 99.34 % 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: 0.47 (0.21), residues: 1479 helix: -0.16 (0.27), residues: 336 sheet: 1.14 (0.27), residues: 319 loop : 0.32 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.009 TRP A 35 HIS 0.009 0.002 HIS E 249 PHE 0.030 0.006 PHE A 383 TYR 0.039 0.007 TYR E 486 ARG 0.007 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 577 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 574 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.9033 (mt) cc_final: 0.8791 (mt) REVERT: A 352 HIS cc_start: 0.8055 (m-70) cc_final: 0.7837 (m170) REVERT: A 377 ASN cc_start: 0.8457 (t0) cc_final: 0.8257 (t0) REVERT: A 426 MET cc_start: 0.8169 (ttm) cc_final: 0.7561 (ttt) REVERT: A 481 SER cc_start: 0.8593 (p) cc_final: 0.8263 (t) REVERT: B 530 MET cc_start: 0.7844 (mtp) cc_final: 0.7502 (mtp) REVERT: B 588 ARG cc_start: 0.7454 (mtt180) cc_final: 0.7153 (tmm-80) REVERT: B 603 ILE cc_start: 0.8448 (pt) cc_final: 0.8117 (pt) REVERT: B 622 ILE cc_start: 0.8777 (mm) cc_final: 0.8304 (mm) REVERT: C 629 LEU cc_start: 0.9254 (mt) cc_final: 0.9025 (mp) REVERT: E 103 GLN cc_start: 0.8608 (tp40) cc_final: 0.8099 (tm-30) REVERT: E 165 TYR cc_start: 0.6089 (t80) cc_final: 0.5349 (t80) REVERT: E 173 VAL cc_start: 0.7409 (t) cc_final: 0.7069 (t) REVERT: E 376 PHE cc_start: 0.8614 (m-80) cc_final: 0.8385 (m-10) REVERT: D 545 LEU cc_start: 0.8832 (mt) cc_final: 0.8588 (mt) REVERT: D 660 LEU cc_start: 0.7899 (tp) cc_final: 0.7497 (tt) REVERT: F 129 LEU cc_start: 0.8917 (tp) cc_final: 0.8661 (tt) REVERT: F 172 ASP cc_start: 0.7428 (m-30) cc_final: 0.7216 (m-30) REVERT: F 232 LYS cc_start: 0.8500 (mmtt) cc_final: 0.7859 (tptp) REVERT: F 315 GLN cc_start: 0.8227 (mp10) cc_final: 0.7384 (mm-40) REVERT: F 348 GLN cc_start: 0.8168 (mm110) cc_final: 0.7806 (mm-40) outliers start: 3 outliers final: 3 residues processed: 577 average time/residue: 0.5797 time to fit residues: 471.8392 Evaluate side-chains 412 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 409 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain E residue 339 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 249 HIS B 616 ASN B 618 ASN B 625 ASN E 330 HIS F 85 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 14336 Z= 0.222 Angle : 0.688 8.079 19484 Z= 0.361 Chirality : 0.048 0.443 2422 Planarity : 0.004 0.043 2403 Dihedral : 7.874 67.303 3015 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 3.28 % Allowed : 11.01 % Favored : 85.71 % 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: 1479 helix: 0.98 (0.28), residues: 332 sheet: 0.84 (0.26), residues: 333 loop : 0.03 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 623 HIS 0.008 0.001 HIS A 249 PHE 0.027 0.002 PHE B 522 TYR 0.019 0.002 TYR D 643 ARG 0.007 0.001 ARG D 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 485 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 440 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8844 (mt) cc_final: 0.8637 (mt) REVERT: A 335 LYS cc_start: 0.8491 (tttt) cc_final: 0.8136 (tptm) REVERT: A 481 SER cc_start: 0.8386 (p) cc_final: 0.8037 (t) REVERT: B 588 ARG cc_start: 0.7341 (mtt180) cc_final: 0.7090 (tmm-80) REVERT: B 603 ILE cc_start: 0.8443 (pt) cc_final: 0.8088 (pt) REVERT: B 622 ILE cc_start: 0.8696 (mm) cc_final: 0.8387 (mm) REVERT: C 632 ASP cc_start: 0.8456 (t0) cc_final: 0.8254 (t0) REVERT: E 160 LYS cc_start: 0.7536 (ttpt) cc_final: 0.7277 (tmmt) REVERT: E 165 TYR cc_start: 0.6168 (t80) cc_final: 0.5385 (t80) REVERT: E 173 VAL cc_start: 0.7737 (t) cc_final: 0.7403 (t) REVERT: D 545 LEU cc_start: 0.8495 (mt) cc_final: 0.8275 (mt) REVERT: D 629 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8378 (mp) REVERT: D 660 LEU cc_start: 0.7619 (tp) cc_final: 0.7393 (tt) REVERT: F 129 LEU cc_start: 0.8541 (tp) cc_final: 0.8215 (tt) REVERT: F 172 ASP cc_start: 0.7504 (m-30) cc_final: 0.7282 (m-30) REVERT: F 232 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7641 (tptp) outliers start: 45 outliers final: 33 residues processed: 455 average time/residue: 0.5620 time to fit residues: 379.0082 Evaluate side-chains 427 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 393 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 195 ASN B 640 GLN F 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14336 Z= 0.385 Angle : 0.708 5.774 19484 Z= 0.364 Chirality : 0.047 0.388 2422 Planarity : 0.004 0.053 2403 Dihedral : 7.207 58.831 3015 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.86 % Allowed : 12.68 % Favored : 83.45 % 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: 0.08 (0.21), residues: 1479 helix: 1.26 (0.29), residues: 315 sheet: 0.32 (0.27), residues: 354 loop : -0.52 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 45 HIS 0.007 0.002 HIS F 330 PHE 0.023 0.002 PHE B 522 TYR 0.021 0.002 TYR D 643 ARG 0.006 0.001 ARG C 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 402 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.9029 (mt) cc_final: 0.8829 (mt) REVERT: A 335 LYS cc_start: 0.8496 (tttt) cc_final: 0.8129 (tptm) REVERT: A 481 SER cc_start: 0.8701 (p) cc_final: 0.8246 (t) REVERT: B 530 MET cc_start: 0.7576 (mtp) cc_final: 0.7289 (mtp) REVERT: B 588 ARG cc_start: 0.7528 (mtt180) cc_final: 0.7130 (tmm-80) REVERT: B 603 ILE cc_start: 0.8303 (pt) cc_final: 0.7911 (pt) REVERT: B 622 ILE cc_start: 0.8741 (mm) cc_final: 0.8346 (mm) REVERT: E 160 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7556 (tmmt) REVERT: E 173 VAL cc_start: 0.7889 (t) cc_final: 0.7629 (t) REVERT: E 246 GLN cc_start: 0.6143 (mm-40) cc_final: 0.5779 (mm-40) REVERT: E 342 LEU cc_start: 0.7954 (mt) cc_final: 0.7576 (tp) REVERT: D 629 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8449 (mp) REVERT: D 660 LEU cc_start: 0.7941 (tp) cc_final: 0.7578 (tt) REVERT: F 232 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7820 (tptm) outliers start: 53 outliers final: 45 residues processed: 427 average time/residue: 0.5298 time to fit residues: 333.7529 Evaluate side-chains 421 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 375 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 434 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 10.0000 chunk 117 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN F 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 14336 Z= 0.407 Angle : 0.698 7.344 19484 Z= 0.357 Chirality : 0.048 0.394 2422 Planarity : 0.004 0.037 2403 Dihedral : 7.247 59.126 3011 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.17 % Allowed : 13.48 % Favored : 81.34 % 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: -0.59 (0.21), residues: 1479 helix: 0.82 (0.28), residues: 313 sheet: -0.03 (0.27), residues: 332 loop : -1.02 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 631 HIS 0.008 0.002 HIS F 352 PHE 0.018 0.002 PHE F 151 TYR 0.015 0.002 TYR C 638 ARG 0.004 0.001 ARG C 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 380 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.9093 (mt) cc_final: 0.8878 (mt) REVERT: A 335 LYS cc_start: 0.8570 (tttt) cc_final: 0.8214 (tptm) REVERT: A 481 SER cc_start: 0.8767 (p) cc_final: 0.8207 (t) REVERT: B 530 MET cc_start: 0.7934 (mtp) cc_final: 0.7604 (mtp) REVERT: B 588 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7187 (tmm-80) REVERT: B 603 ILE cc_start: 0.8421 (pt) cc_final: 0.8047 (pt) REVERT: B 622 ILE cc_start: 0.8822 (mm) cc_final: 0.8435 (mm) REVERT: E 45 TRP cc_start: 0.8889 (p90) cc_final: 0.8464 (p90) REVERT: E 160 LYS cc_start: 0.7836 (ttpt) cc_final: 0.7506 (tmmt) REVERT: E 165 TYR cc_start: 0.6054 (t80) cc_final: 0.4812 (t80) REVERT: E 173 VAL cc_start: 0.7956 (t) cc_final: 0.7548 (t) REVERT: E 211 GLU cc_start: 0.8320 (tt0) cc_final: 0.8096 (tt0) REVERT: E 246 GLN cc_start: 0.6062 (mm-40) cc_final: 0.5679 (mm-40) REVERT: E 342 LEU cc_start: 0.7956 (mt) cc_final: 0.7483 (tp) REVERT: D 629 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8463 (mp) REVERT: D 660 LEU cc_start: 0.7933 (tp) cc_final: 0.7587 (tt) REVERT: F 95 MET cc_start: 0.8569 (ppp) cc_final: 0.7993 (ptt) REVERT: F 232 LYS cc_start: 0.8502 (mmtt) cc_final: 0.7912 (tptp) outliers start: 71 outliers final: 61 residues processed: 415 average time/residue: 0.5266 time to fit residues: 319.3268 Evaluate side-chains 426 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 364 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 485 LYS Chi-restraints excluded: chain F residue 491 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS F 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14336 Z= 0.207 Angle : 0.569 6.858 19484 Z= 0.291 Chirality : 0.044 0.359 2422 Planarity : 0.003 0.041 2403 Dihedral : 6.516 55.106 3011 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.21 % Allowed : 16.55 % Favored : 80.25 % 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: -0.47 (0.21), residues: 1479 helix: 1.06 (0.29), residues: 319 sheet: -0.12 (0.27), residues: 348 loop : -0.95 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 631 HIS 0.005 0.001 HIS A 374 PHE 0.015 0.001 PHE F 151 TYR 0.014 0.001 TYR E 191 ARG 0.004 0.000 ARG C 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 378 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8576 (tp40) cc_final: 0.8123 (tm-30) REVERT: A 122 LEU cc_start: 0.9097 (mt) cc_final: 0.8875 (mt) REVERT: A 335 LYS cc_start: 0.8527 (tttt) cc_final: 0.8160 (tptm) REVERT: A 481 SER cc_start: 0.8640 (p) cc_final: 0.8029 (t) REVERT: B 530 MET cc_start: 0.7843 (mtp) cc_final: 0.7528 (mtp) REVERT: B 588 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7208 (tmm-80) REVERT: B 603 ILE cc_start: 0.8391 (pt) cc_final: 0.8022 (pt) REVERT: B 622 ILE cc_start: 0.8792 (mm) cc_final: 0.8401 (mm) REVERT: E 45 TRP cc_start: 0.8881 (p90) cc_final: 0.8511 (p90) REVERT: E 160 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7544 (tmmt) REVERT: E 165 TYR cc_start: 0.6101 (t80) cc_final: 0.4794 (t80) REVERT: E 246 GLN cc_start: 0.5859 (mm-40) cc_final: 0.5439 (mm-40) REVERT: E 342 LEU cc_start: 0.7866 (mt) cc_final: 0.7402 (tp) REVERT: D 629 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8418 (mp) REVERT: D 660 LEU cc_start: 0.7784 (tp) cc_final: 0.7464 (tt) REVERT: F 95 MET cc_start: 0.8443 (ppp) cc_final: 0.8031 (ptt) REVERT: F 232 LYS cc_start: 0.8561 (mmtt) cc_final: 0.7955 (tptp) outliers start: 44 outliers final: 40 residues processed: 399 average time/residue: 0.5386 time to fit residues: 317.0723 Evaluate side-chains 407 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 366 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 434 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14336 Z= 0.212 Angle : 0.544 5.474 19484 Z= 0.279 Chirality : 0.043 0.347 2422 Planarity : 0.003 0.041 2403 Dihedral : 6.174 50.341 3011 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.79 % Allowed : 16.03 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1479 helix: 1.25 (0.29), residues: 319 sheet: -0.14 (0.27), residues: 348 loop : -0.97 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 631 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.001 PHE F 151 TYR 0.012 0.001 TYR E 191 ARG 0.003 0.000 ARG C 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 370 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7962 (tp30) REVERT: A 92 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7674 (mm-30) REVERT: A 114 GLN cc_start: 0.8586 (tp40) cc_final: 0.8130 (tm-30) REVERT: A 122 LEU cc_start: 0.9105 (mt) cc_final: 0.8869 (mt) REVERT: A 435 TYR cc_start: 0.9016 (t80) cc_final: 0.8727 (t80) REVERT: B 530 MET cc_start: 0.7723 (mtp) cc_final: 0.7409 (mtp) REVERT: B 588 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7236 (tmm-80) REVERT: B 603 ILE cc_start: 0.8393 (pt) cc_final: 0.8052 (pt) REVERT: B 622 ILE cc_start: 0.8771 (mm) cc_final: 0.8412 (mm) REVERT: C 596 TRP cc_start: 0.7882 (m-10) cc_final: 0.7593 (m-10) REVERT: E 45 TRP cc_start: 0.8913 (p90) cc_final: 0.8597 (p90) REVERT: E 160 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7494 (tmmt) REVERT: E 162 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: E 165 TYR cc_start: 0.6118 (t80) cc_final: 0.4870 (t80) REVERT: E 342 LEU cc_start: 0.7878 (mt) cc_final: 0.7403 (tp) REVERT: D 660 LEU cc_start: 0.7681 (tp) cc_final: 0.7358 (tt) REVERT: F 95 MET cc_start: 0.8465 (ppp) cc_final: 0.8196 (ptt) REVERT: F 129 LEU cc_start: 0.8622 (tp) cc_final: 0.8247 (tt) REVERT: F 232 LYS cc_start: 0.8565 (mmtt) cc_final: 0.7935 (tptp) outliers start: 52 outliers final: 41 residues processed: 392 average time/residue: 0.5327 time to fit residues: 304.2083 Evaluate side-chains 402 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 360 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 162 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 434 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 0.0470 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14336 Z= 0.344 Angle : 0.635 6.976 19484 Z= 0.321 Chirality : 0.045 0.369 2422 Planarity : 0.004 0.038 2403 Dihedral : 6.916 59.078 3011 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.59 % Allowed : 15.38 % Favored : 80.03 % 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: -0.81 (0.21), residues: 1479 helix: 1.00 (0.29), residues: 319 sheet: -0.44 (0.28), residues: 340 loop : -1.22 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 479 HIS 0.006 0.002 HIS A 330 PHE 0.013 0.002 PHE F 151 TYR 0.051 0.002 TYR D 643 ARG 0.004 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 431 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 368 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8005 (tp30) REVERT: A 114 GLN cc_start: 0.8607 (tp40) cc_final: 0.8125 (tm-30) REVERT: A 122 LEU cc_start: 0.9159 (mt) cc_final: 0.8918 (mt) REVERT: B 530 MET cc_start: 0.7910 (mtp) cc_final: 0.7572 (mtp) REVERT: B 588 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7300 (tmm-80) REVERT: B 603 ILE cc_start: 0.8417 (pt) cc_final: 0.8067 (pt) REVERT: B 622 ILE cc_start: 0.8901 (mm) cc_final: 0.8569 (mm) REVERT: C 596 TRP cc_start: 0.7971 (m-10) cc_final: 0.7655 (m-10) REVERT: C 634 GLU cc_start: 0.8589 (tt0) cc_final: 0.8228 (tt0) REVERT: E 45 TRP cc_start: 0.8900 (p90) cc_final: 0.8670 (p90) REVERT: E 160 LYS cc_start: 0.7755 (ttpt) cc_final: 0.7486 (tmmt) REVERT: E 162 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: E 165 TYR cc_start: 0.5888 (t80) cc_final: 0.4759 (t80) REVERT: E 342 LEU cc_start: 0.8026 (mt) cc_final: 0.7530 (tp) REVERT: D 660 LEU cc_start: 0.7764 (tp) cc_final: 0.7460 (tt) REVERT: F 95 MET cc_start: 0.8496 (ppp) cc_final: 0.8266 (ptt) REVERT: F 232 LYS cc_start: 0.8577 (mmtt) cc_final: 0.7951 (tptp) outliers start: 63 outliers final: 53 residues processed: 398 average time/residue: 0.5132 time to fit residues: 297.7594 Evaluate side-chains 412 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 358 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain C residue 591 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 162 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 484 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14336 Z= 0.186 Angle : 0.536 4.860 19484 Z= 0.274 Chirality : 0.043 0.350 2422 Planarity : 0.003 0.039 2403 Dihedral : 6.399 53.104 3011 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.43 % Allowed : 17.49 % Favored : 79.08 % 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: -0.57 (0.21), residues: 1479 helix: 1.23 (0.29), residues: 319 sheet: -0.29 (0.28), residues: 348 loop : -1.09 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 631 HIS 0.005 0.001 HIS A 374 PHE 0.014 0.001 PHE F 151 TYR 0.027 0.001 TYR D 643 ARG 0.004 0.000 ARG F 419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 411 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 364 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7973 (tp30) REVERT: A 114 GLN cc_start: 0.8559 (tp40) cc_final: 0.8153 (tm-30) REVERT: A 122 LEU cc_start: 0.9153 (mt) cc_final: 0.8910 (mt) REVERT: B 530 MET cc_start: 0.7672 (mtp) cc_final: 0.7391 (mtp) REVERT: B 588 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7289 (tmm-80) REVERT: B 603 ILE cc_start: 0.8400 (pt) cc_final: 0.8079 (pt) REVERT: B 622 ILE cc_start: 0.8904 (mm) cc_final: 0.8570 (mm) REVERT: C 596 TRP cc_start: 0.7885 (m-10) cc_final: 0.7579 (m-10) REVERT: E 45 TRP cc_start: 0.8914 (p90) cc_final: 0.8657 (p90) REVERT: E 160 LYS cc_start: 0.7740 (ttpt) cc_final: 0.7480 (tmmt) REVERT: E 162 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7275 (pm20) REVERT: E 165 TYR cc_start: 0.5934 (t80) cc_final: 0.4806 (t80) REVERT: E 342 LEU cc_start: 0.7908 (mt) cc_final: 0.7398 (tp) REVERT: D 660 LEU cc_start: 0.7662 (tp) cc_final: 0.7380 (tt) outliers start: 47 outliers final: 43 residues processed: 383 average time/residue: 0.5671 time to fit residues: 318.9508 Evaluate side-chains 405 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 361 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 591 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 162 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 484 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14336 Z= 0.305 Angle : 0.598 6.734 19484 Z= 0.303 Chirality : 0.045 0.368 2422 Planarity : 0.004 0.036 2403 Dihedral : 6.724 51.197 3011 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.86 % Allowed : 16.91 % Favored : 79.23 % 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: -0.78 (0.21), residues: 1479 helix: 1.18 (0.29), residues: 319 sheet: -0.49 (0.27), residues: 344 loop : -1.24 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 631 HIS 0.007 0.001 HIS A 374 PHE 0.012 0.002 PHE E 53 TYR 0.030 0.002 TYR D 643 ARG 0.007 0.001 ARG C 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 423 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 370 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8163 (p) REVERT: A 91 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8023 (tp30) REVERT: A 114 GLN cc_start: 0.8586 (tp40) cc_final: 0.8123 (tm-30) REVERT: A 122 LEU cc_start: 0.9194 (mt) cc_final: 0.8939 (mt) REVERT: B 530 MET cc_start: 0.7856 (mtp) cc_final: 0.7534 (mtp) REVERT: B 571 TRP cc_start: 0.4956 (OUTLIER) cc_final: 0.4525 (m100) REVERT: B 588 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7310 (tmm-80) REVERT: B 603 ILE cc_start: 0.8403 (pt) cc_final: 0.8085 (pt) REVERT: B 622 ILE cc_start: 0.8896 (mm) cc_final: 0.8527 (mm) REVERT: C 596 TRP cc_start: 0.7954 (m-10) cc_final: 0.7588 (m-10) REVERT: C 634 GLU cc_start: 0.8584 (tt0) cc_final: 0.8242 (tt0) REVERT: E 45 TRP cc_start: 0.8894 (p90) cc_final: 0.8680 (p90) REVERT: E 160 LYS cc_start: 0.7774 (ttpt) cc_final: 0.7505 (tmmt) REVERT: E 162 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: E 165 TYR cc_start: 0.5881 (t80) cc_final: 0.4781 (t80) REVERT: E 342 LEU cc_start: 0.8021 (mt) cc_final: 0.7502 (tp) REVERT: D 660 LEU cc_start: 0.7688 (tp) cc_final: 0.7415 (tt) REVERT: F 467 THR cc_start: 0.8332 (m) cc_final: 0.7970 (p) outliers start: 53 outliers final: 46 residues processed: 391 average time/residue: 0.5258 time to fit residues: 299.9293 Evaluate side-chains 412 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 363 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 591 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 162 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 484 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 171 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 136 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14336 Z= 0.149 Angle : 0.515 5.144 19484 Z= 0.264 Chirality : 0.043 0.335 2422 Planarity : 0.003 0.062 2403 Dihedral : 5.982 53.596 3011 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.33 % Allowed : 18.22 % Favored : 79.45 % 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: -0.43 (0.22), residues: 1479 helix: 1.51 (0.29), residues: 320 sheet: -0.31 (0.28), residues: 353 loop : -1.02 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 631 HIS 0.005 0.001 HIS A 72 PHE 0.014 0.001 PHE F 151 TYR 0.029 0.001 TYR D 643 ARG 0.009 0.000 ARG D 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 395 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 363 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8515 (t) cc_final: 0.8221 (p) REVERT: A 91 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8001 (tp30) REVERT: A 114 GLN cc_start: 0.8500 (tp40) cc_final: 0.8110 (tm-30) REVERT: A 122 LEU cc_start: 0.9179 (mt) cc_final: 0.8924 (mt) REVERT: B 530 MET cc_start: 0.7596 (mtp) cc_final: 0.7298 (mtp) REVERT: B 588 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7121 (tmm-80) REVERT: B 603 ILE cc_start: 0.8329 (pt) cc_final: 0.8079 (pt) REVERT: B 622 ILE cc_start: 0.8903 (mm) cc_final: 0.8549 (mm) REVERT: C 596 TRP cc_start: 0.7903 (m-10) cc_final: 0.7629 (m-10) REVERT: C 641 ILE cc_start: 0.7741 (mp) cc_final: 0.7456 (mp) REVERT: E 45 TRP cc_start: 0.8925 (p90) cc_final: 0.8698 (p90) REVERT: E 160 LYS cc_start: 0.7761 (ttpt) cc_final: 0.7505 (tmmt) REVERT: E 162 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7284 (pm20) REVERT: E 165 TYR cc_start: 0.5830 (t80) cc_final: 0.4763 (t80) REVERT: E 342 LEU cc_start: 0.7861 (mt) cc_final: 0.7346 (tp) REVERT: D 540 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7968 (mp-120) REVERT: F 467 THR cc_start: 0.8199 (m) cc_final: 0.7822 (p) outliers start: 32 outliers final: 29 residues processed: 379 average time/residue: 0.5245 time to fit residues: 290.0103 Evaluate side-chains 389 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 358 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 591 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 162 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 484 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.163367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140673 restraints weight = 62202.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145793 restraints weight = 26138.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.148921 restraints weight = 14559.634| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14336 Z= 0.149 Angle : 0.498 6.015 19484 Z= 0.256 Chirality : 0.042 0.321 2422 Planarity : 0.003 0.037 2403 Dihedral : 5.528 56.013 3011 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.48 % Allowed : 18.08 % Favored : 79.45 % 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: -0.31 (0.22), residues: 1479 helix: 1.72 (0.29), residues: 319 sheet: -0.24 (0.28), residues: 353 loop : -0.98 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 631 HIS 0.005 0.001 HIS A 374 PHE 0.012 0.001 PHE F 151 TYR 0.027 0.001 TYR D 643 ARG 0.005 0.000 ARG F 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6765.85 seconds wall clock time: 121 minutes 46.59 seconds (7306.59 seconds total)