Starting phenix.real_space_refine on Sat May 17 00:01:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2e_40981/05_2025/8t2e_40981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2e_40981/05_2025/8t2e_40981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t2e_40981/05_2025/8t2e_40981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2e_40981/05_2025/8t2e_40981.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2e_40981/05_2025/8t2e_40981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2e_40981/05_2025/8t2e_40981.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9386 2.51 5 N 2574 2.21 5 O 2959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15021 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3392 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 5 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1009 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 946 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "E" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3333 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 401} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 946 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3344 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 7 Chain: "H" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 650 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'TRANS': 129} Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 130 Planarities with less than four sites: {'UNK:plan-1': 130} Unresolved non-hydrogen planarities: 130 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 8.97, per 1000 atoms: 0.60 Number of scatterers: 15021 At special positions: 0 Unit cell: (132.999, 132.999, 117.534, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2959 8.00 N 2574 7.00 C 9386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.09 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.23 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.09 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.01 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.02 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.06 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.10 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 197 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 241 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 289 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 355 " " NAG A 611 " - " ASN A 363 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 448 " " NAG A 614 " - " ASN A 392 " " NAG A 615 " - " ASN A 295 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 241 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 332 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 295 " " NAG E 612 " - " ASN E 386 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 160 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 234 " " NAG F 605 " - " ASN F 241 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 289 " " NAG F 608 " - " ASN F 295 " " NAG F 609 " - " ASN F 301 " " NAG F 610 " - " ASN F 332 " " NAG F 611 " - " ASN F 339 " " NAG F 612 " - " ASN F 355 " " NAG F 613 " - " ASN F 363 " " NAG F 614 " - " ASN F 386 " " NAG F 615 " - " ASN F 448 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN E 156 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN F 262 " Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.4 seconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3532 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 27 sheets defined 26.7% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.043A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.669A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 522 through 528 removed outlier: 4.480A pdb=" N ALA C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 572 through 596 Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 662 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.921A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.206A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.604A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.212A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 537 No H-bonds generated for 'chain 'D' and resid 535 through 537' Processing helix chain 'D' and resid 573 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'F' and resid 67 through 73 Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.026A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 475 through 484 removed outlier: 4.008A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 5.366A pdb=" N UNK H 66 " --> pdb=" O UNK H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'L' and resid 91 through 93 No H-bonds generated for 'chain 'L' and resid 91 through 93' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.351A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.861A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.672A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.144A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 302 removed outlier: 6.688A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 334 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 469 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.458A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.117A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.639A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.933A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 removed outlier: 4.396A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 413 through 421 current: chain 'E' and resid 465 through 470 Processing sheet with id=AB7, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.262A pdb=" N CYS D 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N TYR F 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR D 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL F 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL D 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.558A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.495A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 283 through 302 removed outlier: 6.738A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 329 through 334 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 466 through 470 Processing sheet with id=AC5, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.570A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AC7, first strand: chain 'H' and resid 34 through 41 removed outlier: 5.995A pdb=" N UNK H 39 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N UNK H 47 " --> pdb=" O UNK H 39 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N UNK H 41 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N UNK H 45 " --> pdb=" O UNK H 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 117 through 120 Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'L' and resid 32 through 36 removed outlier: 6.778A pdb=" N UNK L 33 " --> pdb=" O UNK L 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 51 through 52 current: chain 'L' and resid 94 through 97 476 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4294 1.33 - 1.48: 4621 1.48 - 1.63: 6211 1.63 - 1.78: 52 1.78 - 1.93: 91 Bond restraints: 15269 Sorted by residual: bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.509 -0.111 1.60e-02 3.91e+03 4.84e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.79e+01 bond pdb=" NE ARG E 504 " pdb=" CZ ARG E 504 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.49e+01 bond pdb=" CB ILE F 184 " pdb=" CG1 ILE F 184 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" NE ARG F 456 " pdb=" CZ ARG F 456 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.06e+01 ... (remaining 15264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 18601 2.66 - 5.32: 1946 5.32 - 7.98: 192 7.98 - 10.64: 9 10.64 - 13.30: 2 Bond angle restraints: 20750 Sorted by residual: angle pdb=" N GLU E 87 " pdb=" CA GLU E 87 " pdb=" C GLU E 87 " ideal model delta sigma weight residual 111.28 120.05 -8.77 1.09e+00 8.42e-01 6.47e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.58 -8.02 1.01e+00 9.80e-01 6.30e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.01e+00 9.80e-01 5.92e+01 angle pdb=" C ALA A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta sigma weight residual 120.31 127.53 -7.22 9.80e-01 1.04e+00 5.43e+01 angle pdb=" N TRP F 395 " pdb=" CA TRP F 395 " pdb=" C TRP F 395 " ideal model delta sigma weight residual 113.17 122.41 -9.24 1.26e+00 6.30e-01 5.37e+01 ... (remaining 20745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.01: 9725 21.01 - 42.03: 212 42.03 - 63.04: 59 63.04 - 84.06: 29 84.06 - 105.07: 17 Dihedral angle restraints: 10042 sinusoidal: 4637 harmonic: 5405 Sorted by residual: dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 39.05 53.95 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS F 378 " pdb=" SG CYS F 378 " pdb=" SG CYS F 445 " pdb=" CB CYS F 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.79 42.79 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -127.32 41.32 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 10039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1821 0.111 - 0.222: 467 0.222 - 0.333: 184 0.333 - 0.445: 103 0.445 - 0.556: 20 Chirality restraints: 2595 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.20e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.26e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.96e+01 ... (remaining 2592 not shown) Planarity restraints: 2615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 339 " 0.083 2.00e-02 2.50e+03 8.66e-02 9.38e+01 pdb=" CG ASN E 339 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN E 339 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 339 " -0.135 2.00e-02 2.50e+03 pdb=" C1 NAG E 609 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " -0.071 2.00e-02 2.50e+03 7.44e-02 6.92e+01 pdb=" CG ASN A 392 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " 0.115 2.00e-02 2.50e+03 pdb=" C1 NAG A 614 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 160 " 0.066 2.00e-02 2.50e+03 6.86e-02 5.88e+01 pdb=" CG ASN F 160 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN F 160 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN F 160 " -0.106 2.00e-02 2.50e+03 pdb=" C1 NAG F 602 " 0.084 2.00e-02 2.50e+03 ... (remaining 2612 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 5330 2.88 - 3.38: 13209 3.38 - 3.89: 24306 3.89 - 4.39: 27879 4.39 - 4.90: 45093 Nonbonded interactions: 115817 Sorted by model distance: nonbonded pdb=" OG SER E 334 " pdb=" OG1 THR E 337 " model vdw 2.373 3.040 nonbonded pdb=" O THR F 248 " pdb=" CB THR F 248 " model vdw 2.375 2.776 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.416 2.496 nonbonded pdb=" NZ LYS D 574 " pdb=" OD1 ASP F 107 " model vdw 2.430 3.120 nonbonded pdb=" N THR E 240 " pdb=" O THR E 240 " model vdw 2.443 2.496 ... (remaining 115812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 57 or resid 66 through 77 or resid 83 through 1 \ 40 or resid 150 through 163 or resid 165 through 206 or (resid 207 and (name N o \ r name CA or name C or name O or name CB )) or resid 208 through 355 or resid 35 \ 7 through 364 or resid 370 through 395 or resid 412 through 456 or resid 465 thr \ ough 504 or resid 601 through 612)) selection = (chain 'E' and (resid 34 through 77 or resid 83 through 140 or resid 150 through \ 182 or resid 189 through 364 or resid 370 through 456 or resid 465 through 504 \ or resid 601 through 612)) selection = (chain 'F' and (resid 34 through 57 or resid 66 through 163 or resid 165 through \ 182 or resid 189 through 206 or (resid 207 and (name N or name CA or name C or \ name O or name CB )) or resid 208 through 355 or resid 357 through 364 or resid \ 370 through 395 or resid 412 through 456 or resid 465 through 504 or resid 601 t \ hrough 612)) } ncs_group { reference = (chain 'B' and (resid 522 through 663 or resid 701 through 702)) selection = chain 'C' selection = (chain 'D' and (resid 522 through 663 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.390 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.202 15367 Z= 1.207 Angle : 1.692 13.300 21011 Z= 1.075 Chirality : 0.140 0.556 2595 Planarity : 0.009 0.048 2559 Dihedral : 11.270 105.070 6411 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.78 % Favored : 98.09 % Rotamer: Outliers : 0.14 % Allowed : 0.82 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1574 helix: -0.28 (0.24), residues: 425 sheet: 1.04 (0.24), residues: 383 loop : 0.77 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.010 TRP A 479 HIS 0.006 0.002 HIS A 216 PHE 0.028 0.006 PHE F 383 TYR 0.034 0.006 TYR E 191 ARG 0.007 0.001 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.08023 ( 56) link_NAG-ASN : angle 2.67897 ( 168) link_BETA1-4 : bond 0.06661 ( 9) link_BETA1-4 : angle 4.58463 ( 27) hydrogen bonds : bond 0.15220 ( 476) hydrogen bonds : angle 6.82536 ( 1308) SS BOND : bond 0.04203 ( 33) SS BOND : angle 3.14221 ( 66) covalent geometry : bond 0.02262 (15269) covalent geometry : angle 1.66802 (20750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 479 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7692 (m-90) cc_final: 0.7299 (m-90) REVERT: A 100 MET cc_start: 0.9169 (mtp) cc_final: 0.8760 (mtp) REVERT: A 150 MET cc_start: 0.8320 (mmm) cc_final: 0.7961 (tpp) REVERT: A 192 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7071 (mtt90) REVERT: A 289 ASN cc_start: 0.8068 (t0) cc_final: 0.7820 (t0) REVERT: B 635 ILE cc_start: 0.8919 (mm) cc_final: 0.8663 (tt) REVERT: C 626 MET cc_start: 0.8128 (ttm) cc_final: 0.7909 (ttm) REVERT: E 39 TYR cc_start: 0.8895 (m-80) cc_final: 0.8676 (m-80) REVERT: E 275 GLU cc_start: 0.7944 (tt0) cc_final: 0.7598 (tt0) REVERT: E 297 THR cc_start: 0.8172 (m) cc_final: 0.7895 (p) REVERT: E 500 ARG cc_start: 0.4442 (mtm180) cc_final: 0.3728 (ptt90) REVERT: F 103 GLN cc_start: 0.8684 (tt0) cc_final: 0.8476 (tt0) REVERT: F 207 LYS cc_start: 0.8636 (pttt) cc_final: 0.8260 (mmtp) REVERT: F 231 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8491 (mmmt) REVERT: F 248 THR cc_start: 0.8649 (p) cc_final: 0.8437 (p) REVERT: F 264 SER cc_start: 0.8368 (m) cc_final: 0.7858 (m) REVERT: F 482 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7650 (mm-30) outliers start: 2 outliers final: 1 residues processed: 480 average time/residue: 0.3006 time to fit residues: 201.6846 Evaluate side-chains 313 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 197 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 348 GLN A 352 HIS A 356 ASN A 422 GLN B 630 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN F 105 HIS F 170 GLN F 203 GLN F 283 ASN F 348 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.159813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.137589 restraints weight = 19795.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.141616 restraints weight = 10475.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.144189 restraints weight = 6850.424| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15367 Z= 0.170 Angle : 0.704 8.129 21011 Z= 0.347 Chirality : 0.047 0.282 2595 Planarity : 0.004 0.035 2559 Dihedral : 7.855 72.877 3312 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.54 % Allowed : 9.48 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1574 helix: 1.64 (0.28), residues: 384 sheet: 0.91 (0.23), residues: 424 loop : 0.37 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 479 HIS 0.003 0.001 HIS A 352 PHE 0.020 0.002 PHE E 468 TYR 0.020 0.002 TYR E 486 ARG 0.005 0.001 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 56) link_NAG-ASN : angle 2.86633 ( 168) link_BETA1-4 : bond 0.00666 ( 9) link_BETA1-4 : angle 3.02113 ( 27) hydrogen bonds : bond 0.05865 ( 476) hydrogen bonds : angle 5.09669 ( 1308) SS BOND : bond 0.00448 ( 33) SS BOND : angle 1.19173 ( 66) covalent geometry : bond 0.00385 (15269) covalent geometry : angle 0.64771 (20750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 332 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7632 (m-30) cc_final: 0.7262 (m-30) REVERT: A 82 GLN cc_start: 0.7977 (mt0) cc_final: 0.7666 (mt0) REVERT: A 192 ARG cc_start: 0.6917 (mtm180) cc_final: 0.6266 (mtt90) REVERT: A 500 ARG cc_start: 0.7028 (mtt180) cc_final: 0.6404 (mtp-110) REVERT: C 634 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: C 660 LEU cc_start: 0.9032 (tp) cc_final: 0.8809 (tt) REVERT: E 297 THR cc_start: 0.8452 (m) cc_final: 0.8240 (p) REVERT: F 46 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8377 (mmtt) REVERT: F 150 MET cc_start: 0.7082 (ptp) cc_final: 0.6615 (ptt) REVERT: F 207 LYS cc_start: 0.8497 (pttt) cc_final: 0.8141 (mmtp) REVERT: F 327 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7761 (mtp180) REVERT: F 363 ASN cc_start: 0.7361 (t0) cc_final: 0.6872 (p0) REVERT: F 475 MET cc_start: 0.8317 (tpp) cc_final: 0.7943 (mmt) outliers start: 37 outliers final: 24 residues processed: 345 average time/residue: 0.2734 time to fit residues: 136.5121 Evaluate side-chains 312 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 287 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 160 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS E 195 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.157838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.135494 restraints weight = 20015.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.139406 restraints weight = 10775.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.141915 restraints weight = 7144.152| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15367 Z= 0.143 Angle : 0.605 8.056 21011 Z= 0.297 Chirality : 0.045 0.263 2595 Planarity : 0.003 0.036 2559 Dihedral : 6.403 51.975 3312 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.88 % Allowed : 11.26 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1574 helix: 1.70 (0.28), residues: 390 sheet: 0.92 (0.24), residues: 414 loop : 0.14 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 479 HIS 0.003 0.001 HIS E 374 PHE 0.015 0.002 PHE E 53 TYR 0.020 0.002 TYR E 486 ARG 0.006 0.000 ARG A 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 56) link_NAG-ASN : angle 2.49357 ( 168) link_BETA1-4 : bond 0.00600 ( 9) link_BETA1-4 : angle 2.30773 ( 27) hydrogen bonds : bond 0.04794 ( 476) hydrogen bonds : angle 4.67180 ( 1308) SS BOND : bond 0.00259 ( 33) SS BOND : angle 0.86506 ( 66) covalent geometry : bond 0.00329 (15269) covalent geometry : angle 0.55811 (20750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 317 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7176 (m-30) cc_final: 0.6926 (m-30) REVERT: A 78 ASP cc_start: 0.7485 (m-30) cc_final: 0.7272 (m-30) REVERT: A 153 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6339 (tm-30) REVERT: A 192 ARG cc_start: 0.7070 (mtm180) cc_final: 0.6393 (mtt90) REVERT: A 372 THR cc_start: 0.9018 (p) cc_final: 0.8786 (t) REVERT: A 469 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7118 (mmt90) REVERT: A 500 ARG cc_start: 0.7115 (mtt180) cc_final: 0.6468 (mtp-110) REVERT: C 660 LEU cc_start: 0.9030 (tp) cc_final: 0.8802 (tt) REVERT: E 371 VAL cc_start: 0.8723 (m) cc_final: 0.8356 (t) REVERT: E 492 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7960 (mt-10) REVERT: D 634 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7614 (mm-30) REVERT: D 656 ASN cc_start: 0.8253 (m-40) cc_final: 0.8033 (m-40) REVERT: F 150 MET cc_start: 0.7114 (ptp) cc_final: 0.6700 (ptt) REVERT: F 160 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7568 (m110) REVERT: F 207 LYS cc_start: 0.8501 (pttt) cc_final: 0.8017 (mppt) REVERT: F 231 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8287 (mmtt) outliers start: 42 outliers final: 28 residues processed: 335 average time/residue: 0.2729 time to fit residues: 132.7758 Evaluate side-chains 315 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 285 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 93 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 0.0020 chunk 182 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 398 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.157443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.135150 restraints weight = 20090.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.139089 restraints weight = 10777.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.141646 restraints weight = 7114.319| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15367 Z= 0.126 Angle : 0.562 8.605 21011 Z= 0.275 Chirality : 0.044 0.277 2595 Planarity : 0.003 0.038 2559 Dihedral : 5.470 45.953 3312 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.20 % Allowed : 13.67 % Favored : 84.13 % 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: 0.98 (0.21), residues: 1574 helix: 1.77 (0.28), residues: 391 sheet: 0.82 (0.24), residues: 421 loop : 0.04 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.002 0.001 HIS E 374 PHE 0.016 0.002 PHE E 53 TYR 0.021 0.001 TYR E 173 ARG 0.006 0.000 ARG A 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 56) link_NAG-ASN : angle 2.30252 ( 168) link_BETA1-4 : bond 0.00496 ( 9) link_BETA1-4 : angle 2.02589 ( 27) hydrogen bonds : bond 0.04291 ( 476) hydrogen bonds : angle 4.45147 ( 1308) SS BOND : bond 0.00326 ( 33) SS BOND : angle 0.83051 ( 66) covalent geometry : bond 0.00286 (15269) covalent geometry : angle 0.51942 (20750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6513 (tm-30) REVERT: A 192 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6463 (mtt90) REVERT: A 363 ASN cc_start: 0.7449 (p0) cc_final: 0.7194 (p0) REVERT: A 372 THR cc_start: 0.9061 (p) cc_final: 0.8806 (t) REVERT: A 469 ARG cc_start: 0.8055 (mtt-85) cc_final: 0.7111 (mmt90) REVERT: A 500 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6558 (mtp-110) REVERT: C 660 LEU cc_start: 0.9000 (tp) cc_final: 0.8784 (tt) REVERT: E 371 VAL cc_start: 0.8797 (m) cc_final: 0.8450 (t) REVERT: E 500 ARG cc_start: 0.3701 (ptt90) cc_final: 0.3319 (mtp-110) REVERT: D 656 ASN cc_start: 0.8271 (m-40) cc_final: 0.7962 (m-40) REVERT: F 150 MET cc_start: 0.7071 (ptp) cc_final: 0.6637 (ptt) REVERT: F 160 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7528 (m110) REVERT: F 180 ASP cc_start: 0.7257 (m-30) cc_final: 0.7019 (m-30) REVERT: F 207 LYS cc_start: 0.8536 (pttt) cc_final: 0.7996 (mppt) REVERT: F 363 ASN cc_start: 0.7308 (t0) cc_final: 0.6954 (p0) REVERT: F 475 MET cc_start: 0.8102 (mmt) cc_final: 0.7726 (mmt) outliers start: 32 outliers final: 23 residues processed: 313 average time/residue: 0.2759 time to fit residues: 125.4298 Evaluate side-chains 315 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 290 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 426 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN E 425 ASN F 103 GLN F 352 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.129314 restraints weight = 20533.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133097 restraints weight = 11154.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.135567 restraints weight = 7463.655| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 15367 Z= 0.235 Angle : 0.663 10.627 21011 Z= 0.320 Chirality : 0.047 0.259 2595 Planarity : 0.003 0.034 2559 Dihedral : 5.571 42.280 3312 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.05 % Allowed : 12.91 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1574 helix: 1.57 (0.28), residues: 392 sheet: 0.65 (0.24), residues: 415 loop : -0.33 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.004 0.001 HIS F 352 PHE 0.016 0.002 PHE B 522 TYR 0.022 0.002 TYR A 173 ARG 0.006 0.001 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 56) link_NAG-ASN : angle 2.52949 ( 168) link_BETA1-4 : bond 0.00430 ( 9) link_BETA1-4 : angle 1.88245 ( 27) hydrogen bonds : bond 0.04830 ( 476) hydrogen bonds : angle 4.57012 ( 1308) SS BOND : bond 0.00576 ( 33) SS BOND : angle 1.67339 ( 66) covalent geometry : bond 0.00563 (15269) covalent geometry : angle 0.61596 (20750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 300 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7256 (mm-30) REVERT: A 96 TRP cc_start: 0.7888 (m-90) cc_final: 0.7377 (m-90) REVERT: A 153 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: A 192 ARG cc_start: 0.7215 (mtm180) cc_final: 0.6596 (mtm180) REVERT: A 340 GLU cc_start: 0.7969 (tp30) cc_final: 0.7742 (tp30) REVERT: A 363 ASN cc_start: 0.7646 (p0) cc_final: 0.7412 (p0) REVERT: A 372 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8911 (t) REVERT: A 469 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7189 (mmt90) REVERT: A 500 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6804 (mtp-110) REVERT: C 660 LEU cc_start: 0.9001 (tp) cc_final: 0.8790 (tt) REVERT: E 347 LYS cc_start: 0.8450 (tttt) cc_final: 0.8226 (tttm) REVERT: E 371 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8460 (t) REVERT: F 160 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7467 (m110) REVERT: F 207 LYS cc_start: 0.8518 (pttt) cc_final: 0.7976 (mppt) REVERT: F 264 SER cc_start: 0.8663 (m) cc_final: 0.8432 (m) REVERT: F 316 TRP cc_start: 0.8767 (m100) cc_final: 0.8425 (m-90) REVERT: F 363 ASN cc_start: 0.7598 (t0) cc_final: 0.7219 (p0) outliers start: 59 outliers final: 42 residues processed: 322 average time/residue: 0.2769 time to fit residues: 129.1114 Evaluate side-chains 339 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 293 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 370 GLU Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 100 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN D 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.151625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.129161 restraints weight = 20348.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133005 restraints weight = 11018.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.135458 restraints weight = 7340.937| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15367 Z= 0.204 Angle : 0.627 10.281 21011 Z= 0.304 Chirality : 0.046 0.306 2595 Planarity : 0.003 0.033 2559 Dihedral : 5.467 39.576 3312 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.98 % Allowed : 14.08 % Favored : 81.94 % 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: 0.46 (0.20), residues: 1574 helix: 1.52 (0.28), residues: 393 sheet: 0.58 (0.24), residues: 406 loop : -0.44 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 479 HIS 0.003 0.001 HIS E 85 PHE 0.016 0.002 PHE E 53 TYR 0.020 0.002 TYR A 173 ARG 0.006 0.001 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 56) link_NAG-ASN : angle 2.51619 ( 168) link_BETA1-4 : bond 0.00401 ( 9) link_BETA1-4 : angle 1.65579 ( 27) hydrogen bonds : bond 0.04670 ( 476) hydrogen bonds : angle 4.53105 ( 1308) SS BOND : bond 0.00361 ( 33) SS BOND : angle 1.37814 ( 66) covalent geometry : bond 0.00484 (15269) covalent geometry : angle 0.58062 (20750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 292 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7869 (m-90) cc_final: 0.7361 (m-90) REVERT: A 153 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: A 192 ARG cc_start: 0.7137 (mtm180) cc_final: 0.6615 (mtt90) REVERT: A 340 GLU cc_start: 0.7906 (tp30) cc_final: 0.7704 (tp30) REVERT: A 372 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8886 (t) REVERT: A 469 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7183 (mmt90) REVERT: A 500 ARG cc_start: 0.7377 (mtt180) cc_final: 0.6902 (mtp-110) REVERT: B 595 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8559 (tt) REVERT: C 660 LEU cc_start: 0.8987 (tp) cc_final: 0.8776 (tt) REVERT: E 92 GLU cc_start: 0.6781 (tt0) cc_final: 0.6340 (tt0) REVERT: E 100 MET cc_start: 0.9011 (mtm) cc_final: 0.8717 (mtm) REVERT: E 178 ARG cc_start: 0.7262 (ptm-80) cc_final: 0.7043 (ptm-80) REVERT: E 347 LYS cc_start: 0.8492 (tttt) cc_final: 0.8263 (tttm) REVERT: E 371 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8354 (t) REVERT: F 153 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7208 (mt-10) REVERT: F 161 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6973 (ttp) REVERT: F 207 LYS cc_start: 0.8454 (pttt) cc_final: 0.7940 (mppt) REVERT: F 316 TRP cc_start: 0.8777 (m100) cc_final: 0.8452 (m-90) REVERT: F 363 ASN cc_start: 0.7593 (t0) cc_final: 0.7248 (p0) outliers start: 58 outliers final: 43 residues processed: 313 average time/residue: 0.2771 time to fit residues: 124.9943 Evaluate side-chains 338 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 290 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 102 optimal weight: 5.9990 chunk 71 optimal weight: 0.0170 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.152119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.129687 restraints weight = 20338.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.133521 restraints weight = 10965.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135991 restraints weight = 7298.106| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15367 Z= 0.170 Angle : 0.608 10.570 21011 Z= 0.293 Chirality : 0.045 0.302 2595 Planarity : 0.003 0.035 2559 Dihedral : 5.372 40.348 3310 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.64 % Allowed : 14.90 % Favored : 81.46 % 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: 0.44 (0.21), residues: 1574 helix: 1.60 (0.28), residues: 393 sheet: 0.51 (0.24), residues: 406 loop : -0.48 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.002 0.001 HIS E 85 PHE 0.016 0.002 PHE E 53 TYR 0.019 0.002 TYR A 173 ARG 0.006 0.001 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 56) link_NAG-ASN : angle 2.56282 ( 168) link_BETA1-4 : bond 0.00402 ( 9) link_BETA1-4 : angle 1.52463 ( 27) hydrogen bonds : bond 0.04494 ( 476) hydrogen bonds : angle 4.46035 ( 1308) SS BOND : bond 0.00317 ( 33) SS BOND : angle 1.09745 ( 66) covalent geometry : bond 0.00400 (15269) covalent geometry : angle 0.56022 (20750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6514 (tm-30) REVERT: A 192 ARG cc_start: 0.7158 (mtm180) cc_final: 0.6655 (mtt90) REVERT: A 372 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8927 (t) REVERT: A 484 TYR cc_start: 0.8872 (p90) cc_final: 0.8227 (p90) REVERT: A 500 ARG cc_start: 0.7390 (mtt180) cc_final: 0.6953 (mtp-110) REVERT: B 595 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8548 (tt) REVERT: C 660 LEU cc_start: 0.8974 (tp) cc_final: 0.8762 (tt) REVERT: E 92 GLU cc_start: 0.6819 (tt0) cc_final: 0.6351 (tt0) REVERT: E 100 MET cc_start: 0.9024 (mtm) cc_final: 0.8775 (mtm) REVERT: E 178 ARG cc_start: 0.7255 (ptm-80) cc_final: 0.7051 (ttt90) REVERT: E 347 LYS cc_start: 0.8460 (tttt) cc_final: 0.8216 (tttm) REVERT: E 371 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8418 (t) REVERT: F 153 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7205 (mt-10) REVERT: F 160 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7360 (m110) REVERT: F 161 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7063 (ttp) REVERT: F 207 LYS cc_start: 0.8448 (pttt) cc_final: 0.7939 (mppt) REVERT: F 316 TRP cc_start: 0.8754 (m100) cc_final: 0.8409 (m-90) outliers start: 53 outliers final: 39 residues processed: 322 average time/residue: 0.2748 time to fit residues: 128.6340 Evaluate side-chains 328 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 166 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 94 optimal weight: 0.0370 chunk 146 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.153839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.131476 restraints weight = 20294.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135330 restraints weight = 10947.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.137768 restraints weight = 7278.825| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 15367 Z= 0.130 Angle : 0.588 12.869 21011 Z= 0.286 Chirality : 0.044 0.291 2595 Planarity : 0.003 0.041 2559 Dihedral : 5.222 40.423 3310 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.75 % Allowed : 16.21 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.52 (0.21), residues: 1574 helix: 1.75 (0.28), residues: 393 sheet: 0.49 (0.25), residues: 409 loop : -0.45 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 96 HIS 0.002 0.001 HIS E 374 PHE 0.018 0.001 PHE F 361 TYR 0.020 0.001 TYR A 173 ARG 0.008 0.000 ARG A 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 56) link_NAG-ASN : angle 2.43564 ( 168) link_BETA1-4 : bond 0.00414 ( 9) link_BETA1-4 : angle 1.40383 ( 27) hydrogen bonds : bond 0.04108 ( 476) hydrogen bonds : angle 4.34141 ( 1308) SS BOND : bond 0.00347 ( 33) SS BOND : angle 1.30333 ( 66) covalent geometry : bond 0.00303 (15269) covalent geometry : angle 0.54229 (20750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6541 (tm-30) REVERT: A 192 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6649 (mtt90) REVERT: A 372 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8941 (t) REVERT: A 484 TYR cc_start: 0.8869 (p90) cc_final: 0.8246 (p90) REVERT: A 500 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6948 (mtp-110) REVERT: C 660 LEU cc_start: 0.8952 (tp) cc_final: 0.8747 (tt) REVERT: E 92 GLU cc_start: 0.6834 (tt0) cc_final: 0.6373 (tt0) REVERT: E 100 MET cc_start: 0.8989 (mtm) cc_final: 0.8778 (mtm) REVERT: E 347 LYS cc_start: 0.8446 (tttt) cc_final: 0.8200 (tttm) REVERT: F 161 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6999 (ttp) REVERT: F 207 LYS cc_start: 0.8452 (pttt) cc_final: 0.7922 (mppt) REVERT: F 316 TRP cc_start: 0.8721 (m100) cc_final: 0.8401 (m-90) REVERT: F 363 ASN cc_start: 0.7523 (t0) cc_final: 0.7165 (p0) outliers start: 40 outliers final: 32 residues processed: 314 average time/residue: 0.2707 time to fit residues: 123.3745 Evaluate side-chains 321 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 286 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 571 TRP Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 97 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 chunk 168 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.157177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134671 restraints weight = 20394.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138706 restraints weight = 10614.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.141242 restraints weight = 6948.574| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15367 Z= 0.182 Angle : 0.626 11.286 21011 Z= 0.303 Chirality : 0.046 0.366 2595 Planarity : 0.003 0.033 2559 Dihedral : 5.345 39.878 3310 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.82 % Allowed : 17.03 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.39 (0.21), residues: 1574 helix: 1.64 (0.28), residues: 394 sheet: 0.49 (0.25), residues: 393 loop : -0.55 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 96 HIS 0.002 0.001 HIS E 374 PHE 0.016 0.002 PHE E 53 TYR 0.019 0.002 TYR E 173 ARG 0.007 0.001 ARG F 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 56) link_NAG-ASN : angle 2.47526 ( 168) link_BETA1-4 : bond 0.00386 ( 9) link_BETA1-4 : angle 1.46227 ( 27) hydrogen bonds : bond 0.04367 ( 476) hydrogen bonds : angle 4.42553 ( 1308) SS BOND : bond 0.00460 ( 33) SS BOND : angle 1.33560 ( 66) covalent geometry : bond 0.00434 (15269) covalent geometry : angle 0.58188 (20750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: A 192 ARG cc_start: 0.7171 (mtm180) cc_final: 0.6643 (mtt90) REVERT: A 432 GLN cc_start: 0.7988 (mp10) cc_final: 0.7518 (mp10) REVERT: A 500 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6954 (mtp-110) REVERT: C 660 LEU cc_start: 0.8964 (tp) cc_final: 0.8760 (tt) REVERT: E 92 GLU cc_start: 0.6929 (tt0) cc_final: 0.6499 (tt0) REVERT: E 347 LYS cc_start: 0.8430 (tttt) cc_final: 0.8183 (tttm) REVERT: E 358 ILE cc_start: 0.6676 (mt) cc_final: 0.6203 (mm) REVERT: E 484 TYR cc_start: 0.8966 (p90) cc_final: 0.8712 (p90) REVERT: E 500 ARG cc_start: 0.3825 (ptt90) cc_final: 0.3218 (mtp-110) REVERT: D 634 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7650 (mm-30) REVERT: F 150 MET cc_start: 0.7525 (ptp) cc_final: 0.7317 (ptt) REVERT: F 161 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6931 (ttp) REVERT: F 207 LYS cc_start: 0.8475 (pttt) cc_final: 0.7910 (mppt) REVERT: F 316 TRP cc_start: 0.8791 (m100) cc_final: 0.8431 (m-90) REVERT: F 363 ASN cc_start: 0.7623 (t0) cc_final: 0.7180 (p0) outliers start: 41 outliers final: 35 residues processed: 301 average time/residue: 0.2642 time to fit residues: 115.8903 Evaluate side-chains 314 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 84 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 119 optimal weight: 0.0170 chunk 125 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.161852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.139753 restraints weight = 20683.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.143748 restraints weight = 10722.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.146216 restraints weight = 6968.772| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15367 Z= 0.135 Angle : 0.589 11.660 21011 Z= 0.287 Chirality : 0.044 0.340 2595 Planarity : 0.003 0.035 2559 Dihedral : 5.223 45.186 3310 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.82 % Allowed : 17.03 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1574 helix: 1.78 (0.28), residues: 394 sheet: 0.51 (0.25), residues: 397 loop : -0.53 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 96 HIS 0.003 0.001 HIS E 374 PHE 0.015 0.001 PHE E 53 TYR 0.019 0.001 TYR A 173 ARG 0.007 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 56) link_NAG-ASN : angle 2.38079 ( 168) link_BETA1-4 : bond 0.00430 ( 9) link_BETA1-4 : angle 1.35385 ( 27) hydrogen bonds : bond 0.04062 ( 476) hydrogen bonds : angle 4.33307 ( 1308) SS BOND : bond 0.00426 ( 33) SS BOND : angle 1.15101 ( 66) covalent geometry : bond 0.00315 (15269) covalent geometry : angle 0.54652 (20750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6564 (tm-30) REVERT: A 192 ARG cc_start: 0.7163 (mtm180) cc_final: 0.6657 (mtt90) REVERT: A 246 GLN cc_start: 0.8483 (mt0) cc_final: 0.8089 (mm-40) REVERT: A 432 GLN cc_start: 0.7901 (mp10) cc_final: 0.7348 (mp10) REVERT: A 469 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7344 (mmt90) REVERT: A 484 TYR cc_start: 0.8936 (p90) cc_final: 0.8324 (p90) REVERT: A 500 ARG cc_start: 0.7327 (mtt180) cc_final: 0.6938 (mtp-110) REVERT: B 595 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8529 (tt) REVERT: E 92 GLU cc_start: 0.6907 (tt0) cc_final: 0.6463 (mt-10) REVERT: E 347 LYS cc_start: 0.8416 (tttt) cc_final: 0.8173 (tttm) REVERT: E 500 ARG cc_start: 0.3689 (ptt90) cc_final: 0.3110 (mtp-110) REVERT: D 596 TRP cc_start: 0.8988 (m-10) cc_final: 0.8759 (m-10) REVERT: D 634 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7596 (mm-30) REVERT: F 150 MET cc_start: 0.7382 (ptp) cc_final: 0.7165 (ptt) REVERT: F 161 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7072 (ttp) REVERT: F 169 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7490 (mtpt) REVERT: F 207 LYS cc_start: 0.8486 (pttt) cc_final: 0.7929 (mppt) REVERT: F 316 TRP cc_start: 0.8781 (m100) cc_final: 0.8400 (m-90) REVERT: F 363 ASN cc_start: 0.7609 (t0) cc_final: 0.7080 (p0) outliers start: 41 outliers final: 34 residues processed: 305 average time/residue: 0.2672 time to fit residues: 118.0577 Evaluate side-chains 314 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 174 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 0.0670 chunk 148 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 144 optimal weight: 0.0870 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 656 ASN F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.161874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139388 restraints weight = 20487.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.143497 restraints weight = 10562.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.146117 restraints weight = 6906.417| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15367 Z= 0.097 Angle : 0.557 10.059 21011 Z= 0.271 Chirality : 0.043 0.306 2595 Planarity : 0.003 0.036 2559 Dihedral : 4.931 43.548 3310 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.79 % Allowed : 18.27 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.70 (0.21), residues: 1574 helix: 1.99 (0.28), residues: 394 sheet: 0.67 (0.25), residues: 412 loop : -0.43 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 35 HIS 0.003 0.000 HIS E 374 PHE 0.015 0.001 PHE E 53 TYR 0.019 0.001 TYR A 173 ARG 0.007 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 56) link_NAG-ASN : angle 2.28408 ( 168) link_BETA1-4 : bond 0.00470 ( 9) link_BETA1-4 : angle 1.26418 ( 27) hydrogen bonds : bond 0.03541 ( 476) hydrogen bonds : angle 4.20608 ( 1308) SS BOND : bond 0.00386 ( 33) SS BOND : angle 1.01097 ( 66) covalent geometry : bond 0.00211 (15269) covalent geometry : angle 0.51673 (20750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4824.04 seconds wall clock time: 85 minutes 17.11 seconds (5117.11 seconds total)