Starting phenix.real_space_refine on Fri Jun 13 13:00:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2e_40981/06_2025/8t2e_40981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2e_40981/06_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_40981/06_2025/8t2e_40981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2e_40981/06_2025/8t2e_40981.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2e_40981/06_2025/8t2e_40981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2e_40981/06_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-5710/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: 10.43, per 1000 atoms: 0.69 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: 4.85 Conformation dependent library (CDL) restraints added in 1.8 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: 1.82 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: 5.11 Time building geometry restraints manager: 5.67 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: 57.330 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 39.520 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.630 ------------------------------------------------------------------------------- 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 : 1.656 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: 0.3934 time to fit residues: 268.5356 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 : 2.087 ------------------------------------------------------------------------------- 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 = 19795.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.141610 restraints weight = 10476.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.144238 restraints weight = 6854.276| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 1.504 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: 0.7628 (m-30) cc_final: 0.7257 (m-30) REVERT: A 82 GLN cc_start: 0.7976 (mt0) cc_final: 0.7666 (mt0) REVERT: A 192 ARG cc_start: 0.6916 (mtm180) cc_final: 0.6269 (mtt90) REVERT: A 500 ARG cc_start: 0.7028 (mtt180) cc_final: 0.6407 (mtp-110) REVERT: C 634 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: C 660 LEU cc_start: 0.9033 (tp) cc_final: 0.8810 (tt) REVERT: E 297 THR cc_start: 0.8453 (m) cc_final: 0.8241 (p) REVERT: F 46 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8377 (mmtt) REVERT: F 150 MET cc_start: 0.7080 (ptp) cc_final: 0.6612 (ptt) REVERT: F 207 LYS cc_start: 0.8495 (pttt) cc_final: 0.8142 (mmtp) REVERT: F 327 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7763 (mtp180) REVERT: F 363 ASN cc_start: 0.7361 (t0) cc_final: 0.6870 (p0) REVERT: F 475 MET cc_start: 0.8316 (tpp) cc_final: 0.7944 (mmt) outliers start: 37 outliers final: 24 residues processed: 345 average time/residue: 0.2719 time to fit residues: 136.2165 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 : 1.470 ------------------------------------------------------------------------------- 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: 0.7980 chunk 138 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 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** F 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.158877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136440 restraints weight = 19993.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.140372 restraints weight = 10777.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.142963 restraints weight = 7154.108| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15367 Z= 0.145 Angle : 0.610 7.942 21011 Z= 0.298 Chirality : 0.045 0.251 2595 Planarity : 0.003 0.036 2559 Dihedral : 6.521 53.888 3312 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.75 % Allowed : 11.33 % Favored : 85.92 % 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: 1.07 (0.21), residues: 1574 helix: 1.69 (0.28), residues: 390 sheet: 0.93 (0.24), residues: 414 loop : 0.17 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 479 HIS 0.002 0.001 HIS E 374 PHE 0.015 0.002 PHE E 53 TYR 0.021 0.002 TYR E 486 ARG 0.006 0.000 ARG A 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 56) link_NAG-ASN : angle 2.53065 ( 168) link_BETA1-4 : bond 0.00593 ( 9) link_BETA1-4 : angle 2.37137 ( 27) hydrogen bonds : bond 0.04871 ( 476) hydrogen bonds : angle 4.70257 ( 1308) SS BOND : bond 0.00316 ( 33) SS BOND : angle 0.91289 ( 66) covalent geometry : bond 0.00331 (15269) covalent geometry : angle 0.56152 (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 357 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 317 time to evaluate : 1.565 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: 0.7128 (m-30) cc_final: 0.6887 (m-30) REVERT: A 78 ASP cc_start: 0.7496 (m-30) cc_final: 0.7161 (m-30) REVERT: A 153 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: A 192 ARG cc_start: 0.7067 (mtm180) cc_final: 0.6382 (mtt90) REVERT: A 372 THR cc_start: 0.9009 (p) cc_final: 0.8777 (t) REVERT: A 469 ARG cc_start: 0.8083 (mtt-85) cc_final: 0.7097 (mmt90) REVERT: A 500 ARG cc_start: 0.7113 (mtt180) cc_final: 0.6457 (mtp-110) REVERT: C 660 LEU cc_start: 0.9034 (tp) cc_final: 0.8812 (tt) REVERT: E 371 VAL cc_start: 0.8757 (m) cc_final: 0.8417 (t) REVERT: E 492 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7968 (mt-10) REVERT: D 634 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7622 (mm-30) REVERT: D 656 ASN cc_start: 0.8266 (m-40) cc_final: 0.8045 (m-40) REVERT: F 150 MET cc_start: 0.7111 (ptp) cc_final: 0.6697 (ptt) REVERT: F 160 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7583 (m110) REVERT: F 207 LYS cc_start: 0.8499 (pttt) cc_final: 0.8026 (mppt) REVERT: F 231 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8285 (mmtt) REVERT: F 475 MET cc_start: 0.8158 (tpp) cc_final: 0.7870 (mmt) outliers start: 40 outliers final: 27 residues processed: 334 average time/residue: 0.2682 time to fit residues: 131.5013 Evaluate side-chains 322 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 293 time to evaluate : 1.636 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 82 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 62 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 F 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.156486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.134128 restraints weight = 20156.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.138044 restraints weight = 10859.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.140542 restraints weight = 7181.463| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15367 Z= 0.143 Angle : 0.574 8.507 21011 Z= 0.280 Chirality : 0.045 0.316 2595 Planarity : 0.003 0.038 2559 Dihedral : 5.499 45.971 3312 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.82 % Allowed : 13.12 % Favored : 84.07 % 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: 0.94 (0.21), residues: 1574 helix: 1.71 (0.28), residues: 391 sheet: 0.82 (0.24), residues: 425 loop : 0.01 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 479 HIS 0.003 0.001 HIS E 374 PHE 0.016 0.002 PHE E 53 TYR 0.026 0.002 TYR F 486 ARG 0.007 0.001 ARG A 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 56) link_NAG-ASN : angle 2.31049 ( 168) link_BETA1-4 : bond 0.00500 ( 9) link_BETA1-4 : angle 2.00798 ( 27) hydrogen bonds : bond 0.04412 ( 476) hydrogen bonds : angle 4.46732 ( 1308) SS BOND : bond 0.00270 ( 33) SS BOND : angle 0.85780 ( 66) covalent geometry : bond 0.00329 (15269) covalent geometry : angle 0.53179 (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 345 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 1.618 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 96 TRP cc_start: 0.7854 (m-90) cc_final: 0.7296 (m-90) REVERT: A 153 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: A 192 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6469 (mtt90) REVERT: A 363 ASN cc_start: 0.7701 (p0) cc_final: 0.7371 (p0) REVERT: A 372 THR cc_start: 0.9057 (p) cc_final: 0.8780 (t) REVERT: A 469 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7128 (mmt90) REVERT: A 500 ARG cc_start: 0.7130 (mtt180) cc_final: 0.6560 (mtp-110) REVERT: C 660 LEU cc_start: 0.9005 (tp) cc_final: 0.8788 (tt) REVERT: E 100 MET cc_start: 0.9036 (mtp) cc_final: 0.8584 (mtm) REVERT: E 371 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8480 (t) REVERT: E 482 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7627 (mm-30) REVERT: E 492 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7967 (mt-10) REVERT: E 500 ARG cc_start: 0.3554 (ptt90) cc_final: 0.3154 (mtp-110) REVERT: D 656 ASN cc_start: 0.8284 (m-40) cc_final: 0.7998 (m-40) REVERT: F 150 MET cc_start: 0.7082 (ptp) cc_final: 0.6638 (ptt) REVERT: F 160 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7548 (m110) REVERT: F 180 ASP cc_start: 0.7278 (m-30) cc_final: 0.7038 (m-30) REVERT: F 207 LYS cc_start: 0.8530 (pttt) cc_final: 0.8001 (mppt) REVERT: F 363 ASN cc_start: 0.7435 (t0) cc_final: 0.7017 (p0) REVERT: F 475 MET cc_start: 0.8149 (tpp) cc_final: 0.7884 (mmt) outliers start: 41 outliers final: 28 residues processed: 318 average time/residue: 0.2752 time to fit residues: 127.0515 Evaluate side-chains 321 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 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 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 139 THR Chi-restraints excluded: chain E residue 180 ASP 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 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 333 VAL 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: 8.9990 chunk 93 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.154370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.132036 restraints weight = 20359.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135904 restraints weight = 10916.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.138403 restraints weight = 7212.804| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15367 Z= 0.162 Angle : 0.576 8.713 21011 Z= 0.280 Chirality : 0.045 0.286 2595 Planarity : 0.003 0.036 2559 Dihedral : 5.162 42.008 3310 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.50 % Allowed : 13.32 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1574 helix: 1.64 (0.28), residues: 397 sheet: 0.78 (0.24), residues: 419 loop : -0.17 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 479 HIS 0.003 0.001 HIS F 352 PHE 0.015 0.002 PHE E 53 TYR 0.018 0.002 TYR E 173 ARG 0.006 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 56) link_NAG-ASN : angle 2.41945 ( 168) link_BETA1-4 : bond 0.00427 ( 9) link_BETA1-4 : angle 1.79301 ( 27) hydrogen bonds : bond 0.04366 ( 476) hydrogen bonds : angle 4.42461 ( 1308) SS BOND : bond 0.00295 ( 33) SS BOND : angle 0.85044 ( 66) covalent geometry : bond 0.00381 (15269) covalent geometry : angle 0.53111 (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 358 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 1.495 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 92 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7192 (mm-30) REVERT: A 96 TRP cc_start: 0.7818 (m-90) cc_final: 0.7288 (m-90) REVERT: A 153 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: A 192 ARG cc_start: 0.7178 (mtm180) cc_final: 0.6599 (mtm180) REVERT: A 340 GLU cc_start: 0.7971 (tp30) cc_final: 0.7718 (tp30) REVERT: A 372 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8770 (t) REVERT: A 469 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7127 (mmt90) REVERT: A 500 ARG cc_start: 0.7359 (mtt180) cc_final: 0.6779 (mtp-110) REVERT: C 660 LEU cc_start: 0.8981 (tp) cc_final: 0.8773 (tt) REVERT: E 100 MET cc_start: 0.9139 (mtp) cc_final: 0.8668 (mtm) REVERT: E 371 VAL cc_start: 0.8815 (m) cc_final: 0.8452 (t) REVERT: E 457 ASP cc_start: 0.6962 (m-30) cc_final: 0.6734 (m-30) REVERT: E 482 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7401 (mm-30) REVERT: E 492 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7938 (mt-10) REVERT: D 647 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: F 160 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7495 (m110) REVERT: F 180 ASP cc_start: 0.7445 (m-30) cc_final: 0.7212 (m-30) REVERT: F 207 LYS cc_start: 0.8546 (pttt) cc_final: 0.8001 (mppt) REVERT: F 231 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8368 (mmmt) REVERT: F 264 SER cc_start: 0.8660 (m) cc_final: 0.8403 (m) REVERT: F 363 ASN cc_start: 0.7484 (t0) cc_final: 0.7083 (p0) REVERT: F 475 MET cc_start: 0.8113 (tpp) cc_final: 0.7861 (mmt) outliers start: 51 outliers final: 36 residues processed: 327 average time/residue: 0.2692 time to fit residues: 128.4517 Evaluate side-chains 340 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 231 LYS 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 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL 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: 0.9980 chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 178 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 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 = 0.3648 r_free = 0.3648 target = 0.152873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130393 restraints weight = 20399.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.134229 restraints weight = 11064.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.136723 restraints weight = 7363.612| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3828 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= 0.168 Angle : 0.593 10.566 21011 Z= 0.288 Chirality : 0.045 0.301 2595 Planarity : 0.003 0.035 2559 Dihedral : 5.141 38.420 3310 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.78 % Allowed : 13.74 % Favored : 82.49 % 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: 0.63 (0.21), residues: 1574 helix: 1.67 (0.28), residues: 393 sheet: 0.68 (0.24), residues: 406 loop : -0.34 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.003 0.001 HIS F 72 PHE 0.016 0.002 PHE E 53 TYR 0.017 0.002 TYR F 486 ARG 0.007 0.001 ARG A 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 56) link_NAG-ASN : angle 2.40420 ( 168) link_BETA1-4 : bond 0.00392 ( 9) link_BETA1-4 : angle 1.58632 ( 27) hydrogen bonds : bond 0.04383 ( 476) hydrogen bonds : angle 4.38708 ( 1308) SS BOND : bond 0.00415 ( 33) SS BOND : angle 0.87483 ( 66) covalent geometry : bond 0.00398 (15269) covalent geometry : angle 0.55114 (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 361 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 306 time to evaluate : 1.720 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 96 TRP cc_start: 0.7873 (m-90) cc_final: 0.7668 (m-90) REVERT: A 153 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: A 192 ARG cc_start: 0.7169 (mtm180) cc_final: 0.6588 (mtt90) REVERT: A 340 GLU cc_start: 0.7904 (tp30) cc_final: 0.7703 (tp30) REVERT: A 500 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6852 (mtp-110) REVERT: C 660 LEU cc_start: 0.8961 (tp) cc_final: 0.8757 (tt) REVERT: E 92 GLU cc_start: 0.6743 (tt0) cc_final: 0.6297 (tt0) REVERT: E 100 MET cc_start: 0.9154 (mtp) cc_final: 0.8748 (mtm) REVERT: E 178 ARG cc_start: 0.7161 (ptm-80) cc_final: 0.6933 (ptm-80) REVERT: E 347 LYS cc_start: 0.8438 (tttt) cc_final: 0.8224 (tttm) REVERT: E 371 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8437 (t) REVERT: E 457 ASP cc_start: 0.7123 (m-30) cc_final: 0.6882 (m-30) REVERT: E 492 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7951 (mt-10) REVERT: F 161 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6863 (ttp) REVERT: F 207 LYS cc_start: 0.8499 (pttt) cc_final: 0.7938 (mppt) REVERT: F 264 SER cc_start: 0.8675 (m) cc_final: 0.8454 (m) REVERT: F 316 TRP cc_start: 0.8803 (m100) cc_final: 0.8458 (m-90) REVERT: F 363 ASN cc_start: 0.7586 (t0) cc_final: 0.7176 (p0) outliers start: 55 outliers final: 40 residues processed: 330 average time/residue: 0.3163 time to fit residues: 154.1054 Evaluate side-chains 335 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 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 443 ILE Chi-restraints excluded: chain A residue 466 GLU 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 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 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL 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 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 277 ILE Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 370 GLU Chi-restraints excluded: chain F residue 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: 6.9990 chunk 71 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.154740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.132380 restraints weight = 20220.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.136279 restraints weight = 10870.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.138769 restraints weight = 7222.200| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15367 Z= 0.133 Angle : 0.581 19.270 21011 Z= 0.277 Chirality : 0.046 0.591 2595 Planarity : 0.003 0.034 2559 Dihedral : 4.994 39.115 3310 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.37 % Allowed : 14.90 % Favored : 81.73 % Cbeta Deviations : 0.06 % 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: 0.64 (0.21), residues: 1574 helix: 1.77 (0.28), residues: 393 sheet: 0.61 (0.25), residues: 410 loop : -0.34 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 96 HIS 0.002 0.001 HIS E 374 PHE 0.016 0.001 PHE E 53 TYR 0.015 0.001 TYR E 173 ARG 0.006 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 56) link_NAG-ASN : angle 2.92314 ( 168) link_BETA1-4 : bond 0.00419 ( 9) link_BETA1-4 : angle 1.43232 ( 27) hydrogen bonds : bond 0.04028 ( 476) hydrogen bonds : angle 4.29935 ( 1308) SS BOND : bond 0.00272 ( 33) SS BOND : angle 0.93973 ( 66) covalent geometry : bond 0.00306 (15269) covalent geometry : angle 0.51662 (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 351 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 302 time to evaluate : 1.639 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 96 TRP cc_start: 0.7815 (m-90) cc_final: 0.7592 (m-90) REVERT: A 153 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: A 192 ARG cc_start: 0.7167 (mtm180) cc_final: 0.6667 (mtt90) REVERT: A 484 TYR cc_start: 0.8944 (p90) cc_final: 0.8266 (p90) REVERT: A 500 ARG cc_start: 0.7379 (mtt180) cc_final: 0.6918 (mtp-110) REVERT: B 595 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8556 (tt) REVERT: C 660 LEU cc_start: 0.8957 (tp) cc_final: 0.8752 (tt) REVERT: E 92 GLU cc_start: 0.6730 (tt0) cc_final: 0.6283 (tt0) REVERT: E 100 MET cc_start: 0.9129 (mtp) cc_final: 0.8754 (mtm) REVERT: E 150 MET cc_start: 0.6951 (mmm) cc_final: 0.6721 (tpp) REVERT: E 347 LYS cc_start: 0.8456 (tttt) cc_final: 0.8242 (tttm) REVERT: E 371 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8408 (t) REVERT: E 457 ASP cc_start: 0.7056 (m-30) cc_final: 0.6797 (m-30) REVERT: E 482 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7416 (mm-30) REVERT: E 492 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7889 (mt-10) REVERT: E 500 ARG cc_start: 0.3751 (ptt90) cc_final: 0.3325 (mtp-110) REVERT: F 161 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6851 (ttp) REVERT: F 207 LYS cc_start: 0.8446 (pttt) cc_final: 0.7924 (mppt) REVERT: F 264 SER cc_start: 0.8695 (m) cc_final: 0.8465 (m) REVERT: F 316 TRP cc_start: 0.8753 (m100) cc_final: 0.8497 (m-90) REVERT: F 363 ASN cc_start: 0.7540 (t0) cc_final: 0.7169 (p0) outliers start: 49 outliers final: 38 residues processed: 322 average time/residue: 0.2740 time to fit residues: 128.8653 Evaluate side-chains 330 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER 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 529 THR 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 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 208 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 161 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL 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: 4.9990 chunk 129 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 4 optimal weight: 0.0030 chunk 25 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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 ** 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 = 0.3662 r_free = 0.3662 target = 0.154308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131915 restraints weight = 20297.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.135791 restraints weight = 10940.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.138305 restraints weight = 7284.451| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15367 Z= 0.139 Angle : 0.574 19.768 21011 Z= 0.275 Chirality : 0.044 0.374 2595 Planarity : 0.003 0.034 2559 Dihedral : 5.053 42.216 3310 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.16 % Allowed : 15.52 % Favored : 81.32 % 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: 0.61 (0.21), residues: 1574 helix: 1.76 (0.28), residues: 393 sheet: 0.59 (0.25), residues: 407 loop : -0.36 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 596 HIS 0.002 0.001 HIS E 374 PHE 0.016 0.001 PHE E 53 TYR 0.014 0.001 TYR E 173 ARG 0.005 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 56) link_NAG-ASN : angle 2.77295 ( 168) link_BETA1-4 : bond 0.00404 ( 9) link_BETA1-4 : angle 1.40411 ( 27) hydrogen bonds : bond 0.03995 ( 476) hydrogen bonds : angle 4.28843 ( 1308) SS BOND : bond 0.00281 ( 33) SS BOND : angle 0.87124 ( 66) covalent geometry : bond 0.00323 (15269) covalent geometry : angle 0.51604 (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 341 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 295 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7874 (m-90) cc_final: 0.7645 (m-90) REVERT: A 153 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6482 (tm-30) REVERT: A 192 ARG cc_start: 0.7079 (mtm180) cc_final: 0.6626 (mtt90) REVERT: A 469 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.8051 (mtt-85) REVERT: A 484 TYR cc_start: 0.8938 (p90) cc_final: 0.8277 (p90) REVERT: A 500 ARG cc_start: 0.7422 (mtt180) cc_final: 0.6972 (mtp-110) REVERT: E 92 GLU cc_start: 0.6875 (tt0) cc_final: 0.6369 (tt0) REVERT: E 100 MET cc_start: 0.9161 (mtp) cc_final: 0.8816 (mtm) REVERT: E 347 LYS cc_start: 0.8462 (tttt) cc_final: 0.8224 (tttm) REVERT: E 371 VAL cc_start: 0.8705 (m) cc_final: 0.8283 (t) REVERT: E 482 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7379 (mm-30) REVERT: E 492 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7675 (mt-10) REVERT: F 160 ASN cc_start: 0.7715 (OUTLIER) cc_final: 0.7340 (m110) REVERT: F 161 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6940 (ttp) REVERT: F 207 LYS cc_start: 0.8440 (pttt) cc_final: 0.7926 (mppt) REVERT: F 264 SER cc_start: 0.8710 (m) cc_final: 0.8487 (m) REVERT: F 316 TRP cc_start: 0.8736 (m100) cc_final: 0.8480 (m-90) REVERT: F 363 ASN cc_start: 0.7533 (t0) cc_final: 0.7147 (p0) outliers start: 46 outliers final: 36 residues processed: 315 average time/residue: 0.2837 time to fit residues: 129.6750 Evaluate side-chains 325 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 443 ILE Chi-restraints excluded: chain A residue 466 GLU 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 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 198 THR 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 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 160 ASN Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL 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: 1.9990 chunk 182 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 ** 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 = 0.3700 r_free = 0.3700 target = 0.155958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133583 restraints weight = 20430.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.137504 restraints weight = 10607.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.140026 restraints weight = 7013.409| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15367 Z= 0.223 Angle : 0.666 18.113 21011 Z= 0.318 Chirality : 0.047 0.421 2595 Planarity : 0.003 0.031 2559 Dihedral : 5.575 44.765 3310 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.50 % Allowed : 14.97 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1574 helix: 1.48 (0.27), residues: 394 sheet: 0.46 (0.25), residues: 398 loop : -0.59 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 596 HIS 0.003 0.001 HIS E 85 PHE 0.017 0.002 PHE E 53 TYR 0.021 0.002 TYR A 173 ARG 0.008 0.001 ARG E 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 56) link_NAG-ASN : angle 2.87849 ( 168) link_BETA1-4 : bond 0.00380 ( 9) link_BETA1-4 : angle 1.53688 ( 27) hydrogen bonds : bond 0.04710 ( 476) hydrogen bonds : angle 4.55047 ( 1308) SS BOND : bond 0.00402 ( 33) SS BOND : angle 1.10117 ( 66) covalent geometry : bond 0.00531 (15269) covalent geometry : angle 0.61256 (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 339 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 2.723 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: 0.6999 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: A 192 ARG cc_start: 0.7190 (mtm180) cc_final: 0.6652 (mtt90) REVERT: A 432 GLN cc_start: 0.8000 (mp10) cc_final: 0.7502 (mp10) REVERT: A 500 ARG cc_start: 0.7316 (mtt180) cc_final: 0.6950 (mtp-110) REVERT: E 92 GLU cc_start: 0.6917 (tt0) cc_final: 0.6489 (mt-10) REVERT: E 100 MET cc_start: 0.9238 (mtp) cc_final: 0.8969 (mtm) REVERT: E 347 LYS cc_start: 0.8437 (tttt) cc_final: 0.8181 (tttm) REVERT: E 390 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8341 (mp) REVERT: E 482 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7506 (mm-30) REVERT: E 500 ARG cc_start: 0.3936 (ptt90) cc_final: 0.3209 (mtp-110) REVERT: D 634 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7739 (mm-30) REVERT: F 160 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7284 (m110) REVERT: F 161 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6981 (ttp) REVERT: F 207 LYS cc_start: 0.8513 (pttt) cc_final: 0.7937 (mppt) REVERT: F 264 SER cc_start: 0.8653 (m) cc_final: 0.8450 (m) REVERT: F 316 TRP cc_start: 0.8816 (m100) cc_final: 0.8450 (m-90) outliers start: 51 outliers final: 41 residues processed: 309 average time/residue: 0.2920 time to fit residues: 132.1413 Evaluate side-chains 315 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 270 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET 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 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 443 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 641 ILE 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 172 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 198 THR 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 390 LEU 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 160 ASN Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 370 GLU Chi-restraints excluded: chain F residue 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: 3.9990 chunk 144 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 177 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN E 99 ASN E 203 GLN D 656 ASN F 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.152296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.129466 restraints weight = 20336.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.133342 restraints weight = 11084.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135879 restraints weight = 7433.774| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15367 Z= 0.139 Angle : 0.602 18.624 21011 Z= 0.287 Chirality : 0.045 0.430 2595 Planarity : 0.003 0.035 2559 Dihedral : 5.345 46.192 3310 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.82 % Allowed : 16.07 % Favored : 81.11 % 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: 0.39 (0.21), residues: 1574 helix: 1.70 (0.28), residues: 394 sheet: 0.49 (0.25), residues: 395 loop : -0.58 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 631 HIS 0.002 0.001 HIS E 374 PHE 0.016 0.001 PHE E 53 TYR 0.019 0.001 TYR A 173 ARG 0.005 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 56) link_NAG-ASN : angle 2.81898 ( 168) link_BETA1-4 : bond 0.00423 ( 9) link_BETA1-4 : angle 1.37237 ( 27) hydrogen bonds : bond 0.04133 ( 476) hydrogen bonds : angle 4.38206 ( 1308) SS BOND : bond 0.00299 ( 33) SS BOND : angle 0.87521 ( 66) covalent geometry : bond 0.00322 (15269) covalent geometry : angle 0.54608 (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 322 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6535 (tm-30) REVERT: A 192 ARG cc_start: 0.7165 (mtm180) cc_final: 0.6674 (mtt90) REVERT: A 432 GLN cc_start: 0.7916 (mp10) cc_final: 0.7359 (mp10) REVERT: A 484 TYR cc_start: 0.8904 (p90) cc_final: 0.8273 (p90) REVERT: A 500 ARG cc_start: 0.7306 (mtt180) cc_final: 0.7007 (mtp-110) REVERT: C 623 TRP cc_start: 0.9134 (m100) cc_final: 0.8932 (m100) REVERT: E 92 GLU cc_start: 0.6909 (tt0) cc_final: 0.6472 (mt-10) REVERT: E 100 MET cc_start: 0.9138 (mtp) cc_final: 0.8888 (mtm) REVERT: E 347 LYS cc_start: 0.8451 (tttt) cc_final: 0.8192 (tttm) REVERT: E 390 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8331 (mp) REVERT: E 500 ARG cc_start: 0.3919 (ptt90) cc_final: 0.3291 (mtp-110) REVERT: F 161 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6962 (ttp) REVERT: F 207 LYS cc_start: 0.8433 (pttt) cc_final: 0.7920 (mppt) REVERT: F 264 SER cc_start: 0.8707 (m) cc_final: 0.8499 (m) REVERT: F 316 TRP cc_start: 0.8769 (m100) cc_final: 0.8423 (m-90) REVERT: F 363 ASN cc_start: 0.7541 (t0) cc_final: 0.7108 (p0) outliers start: 41 outliers final: 35 residues processed: 300 average time/residue: 0.2717 time to fit residues: 118.5794 Evaluate side-chains 312 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET 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 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 641 ILE 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 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 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 390 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 161 MET Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 174 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.0040 chunk 53 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.158333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135968 restraints weight = 20524.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139994 restraints weight = 10589.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.142536 restraints weight = 6923.089| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15367 Z= 0.133 Angle : 0.600 18.442 21011 Z= 0.287 Chirality : 0.045 0.399 2595 Planarity : 0.003 0.034 2559 Dihedral : 5.243 46.713 3310 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.75 % Allowed : 16.00 % Favored : 81.25 % 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: 0.46 (0.21), residues: 1574 helix: 1.81 (0.28), residues: 394 sheet: 0.49 (0.25), residues: 396 loop : -0.55 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 35 HIS 0.002 0.001 HIS E 374 PHE 0.016 0.001 PHE E 53 TYR 0.020 0.001 TYR A 173 ARG 0.007 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 56) link_NAG-ASN : angle 2.75103 ( 168) link_BETA1-4 : bond 0.00407 ( 9) link_BETA1-4 : angle 1.34749 ( 27) hydrogen bonds : bond 0.03995 ( 476) hydrogen bonds : angle 4.31926 ( 1308) SS BOND : bond 0.00345 ( 33) SS BOND : angle 1.12523 ( 66) covalent geometry : bond 0.00311 (15269) covalent geometry : angle 0.54535 (20750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5368.48 seconds wall clock time: 94 minutes 42.95 seconds (5682.95 seconds total)