Starting phenix.real_space_refine on Fri Jun 13 06:15:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sww_40823/06_2025/8sww_40823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sww_40823/06_2025/8sww_40823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sww_40823/06_2025/8sww_40823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sww_40823/06_2025/8sww_40823.map" model { file = "/net/cci-nas-00/data/ceres_data/8sww_40823/06_2025/8sww_40823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sww_40823/06_2025/8sww_40823.cif" } resolution = 3.4 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 9229 2.51 5 N 2565 2.21 5 O 2903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 14799 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3478 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "B" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "C" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 927 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3490 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 829 Classifications: {'peptide': 105} Link IDs: {'TRANS': 104} Chain breaks: 2 Chain: "F" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3427 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 3 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "L" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 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: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.74, per 1000 atoms: 0.66 Number of scatterers: 14799 At special positions: 0 Unit cell: (134.03, 139.185, 119.596, 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 2903 8.00 N 2565 7.00 C 9229 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=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 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=2.06 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.12 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.02 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=2.03 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=2.08 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 149 " distance=2.01 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=2.02 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 ALPHA1-3 " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 152 " " NAG A 603 " - " ASN A 289 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 448 " " NAG A 606 " - " ASN A 363 " " NAG A 607 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 618 " " NAG C 702 " - " ASN C 637 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 448 " " NAG E 603 " - " ASN E 332 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 133 " " NAG E 606 " - " ASN E 88 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 152 " " NAG F 603 " - " ASN F 295 " " NAG F 604 " - " ASN F 301 " " NAG F 605 " - " ASN F 339 " " NAG F 606 " - " ASN F 392 " " NAG F 607 " - " ASN F 241 " " NAG F 608 " - " ASN F 276 " " NAG F 609 " - " ASN F 234 " " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN A 386 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN F 262 " " NAG O 1 " - " ASN F 332 " Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 1.7 seconds 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3546 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 27 sheets defined 26.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.590A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.963A pdb=" N ARG A 143 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.168A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.313A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.768A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.722A pdb=" N THR B 536 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 539 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.524A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.220A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 535 Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 570 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 656 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 334 through 350 removed outlier: 4.916A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 474 through 481 removed outlier: 3.532A pdb=" N TRP E 479 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.243A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.740A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 544 Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 638 through 654 Processing helix chain 'F' and resid 98 through 116 removed outlier: 3.593A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.834A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 425 through 429 Processing helix chain 'F' and resid 475 through 480 Processing helix chain 'L' and resid 61 through 64 removed outlier: 3.976A pdb=" N UNK L 64 " --> pdb=" O UNK L 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 61 through 64' Processing helix chain 'L' and resid 83 through 86 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 495 removed outlier: 5.099A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.008A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.349A 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 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 162 through 169 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.455A 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 312 removed outlier: 6.668A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.245A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AB4, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.514A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB5, 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 298 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 330 through 333 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AB6, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.456A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 603 through 604 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: 4.448A 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 161 through 169 removed outlier: 4.518A pdb=" N GLU F 190 " --> pdb=" O ILE F 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 200 through 203 removed outlier: 6.132A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 6.715A 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 284 through 312 removed outlier: 4.359A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 321 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 465 through 470 Processing sheet with id=AC5, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC6, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AC7, first strand: chain 'H' and resid 36 through 41 removed outlier: 5.529A pdb=" N UNK H 36 " --> pdb=" O UNK H 52 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N UNK H 52 " --> pdb=" O UNK H 36 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N UNK H 38 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N UNK H 56 " --> pdb=" O UNK H 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 56 through 57 current: chain 'H' and resid 100 through 101 Processing sheet with id=AC8, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC9, first strand: chain 'L' and resid 32 through 39 removed outlier: 7.360A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 57 through 59 current: chain 'L' and resid 105 through 106 444 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.97 Time building geometry restraints manager: 5.33 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: 3892 1.33 - 1.47: 4556 1.47 - 1.61: 6457 1.61 - 1.75: 22 1.75 - 1.89: 127 Bond restraints: 15054 Sorted by residual: bond pdb=" CB LEU D 568 " pdb=" CG LEU D 568 " ideal model delta sigma weight residual 1.530 1.667 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" NE ARG E 504 " pdb=" CZ ARG E 504 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.59e+01 bond pdb=" CB LEU B 568 " pdb=" CG LEU B 568 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.25e+01 bond pdb=" CB ASN F 289 " pdb=" CG ASN F 289 " ideal model delta sigma weight residual 1.516 1.362 0.154 2.50e-02 1.60e+03 3.78e+01 ... (remaining 15049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 17692 2.37 - 4.73: 2381 4.73 - 7.10: 355 7.10 - 9.47: 40 9.47 - 11.83: 4 Bond angle restraints: 20472 Sorted by residual: angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.60 -8.04 1.01e+00 9.80e-01 6.34e+01 angle pdb=" N TRP D 628 " pdb=" CA TRP D 628 " pdb=" C TRP D 628 " ideal model delta sigma weight residual 110.50 99.80 10.70 1.41e+00 5.03e-01 5.75e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 124.88 -5.22 7.30e-01 1.88e+00 5.12e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 126.62 -7.06 1.01e+00 9.80e-01 4.88e+01 angle pdb=" N VAL A 496 " pdb=" CA VAL A 496 " pdb=" C VAL A 496 " ideal model delta sigma weight residual 111.81 117.68 -5.87 8.60e-01 1.35e+00 4.66e+01 ... (remaining 20467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 9397 21.88 - 43.77: 161 43.77 - 65.65: 47 65.65 - 87.54: 27 87.54 - 109.42: 9 Dihedral angle restraints: 9641 sinusoidal: 4192 harmonic: 5449 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -175.12 89.12 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual 93.00 174.10 -81.10 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -130.47 44.47 1 1.00e+01 1.00e-02 2.75e+01 ... (remaining 9638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1753 0.102 - 0.204: 497 0.204 - 0.306: 138 0.306 - 0.408: 75 0.408 - 0.510: 27 Chirality restraints: 2490 Sorted by residual: 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 -2.65 0.25 2.00e-02 2.50e+03 1.50e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 ... (remaining 2487 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 241 " 0.099 2.00e-02 2.50e+03 1.06e-01 1.40e+02 pdb=" CG ASN F 241 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN F 241 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN F 241 " -0.166 2.00e-02 2.50e+03 pdb=" C1 NAG F 607 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 133 " 0.077 2.00e-02 2.50e+03 8.02e-02 8.05e+01 pdb=" CG ASN E 133 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN E 133 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN E 133 " -0.125 2.00e-02 2.50e+03 pdb=" C1 NAG E 605 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 339 " 0.070 2.00e-02 2.50e+03 7.22e-02 6.52e+01 pdb=" CG ASN F 339 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN F 339 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 339 " -0.111 2.00e-02 2.50e+03 pdb=" C1 NAG F 605 " 0.088 2.00e-02 2.50e+03 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2728 2.76 - 3.30: 13386 3.30 - 3.83: 23299 3.83 - 4.37: 28990 4.37 - 4.90: 46438 Nonbonded interactions: 114841 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.231 3.040 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.386 2.496 nonbonded pdb=" N GLU E 482 " pdb=" O GLU E 482 " model vdw 2.397 2.496 nonbonded pdb=" O4 BMA N 3 " pdb=" O6 BMA N 3 " model vdw 2.403 3.040 nonbonded pdb=" OD2 ASP C 632 " pdb=" NZ LYS E 46 " model vdw 2.422 3.120 ... (remaining 114836 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 36 through 58 or resid 66 through 411 or resid 413 through \ 501 or resid 602 through 607)) selection = (chain 'E' and (resid 36 through 154 or resid 159 through 176 or resid 189 throu \ gh 501 or resid 601 through 606)) selection = (chain 'F' and (resid 36 through 154 or resid 159 through 176 or resid 189 throu \ gh 398 or resid 413 through 501 or resid 604 through 609)) } ncs_group { reference = (chain 'B' and (resid 522 through 547 or resid 569 through 608 or resid 620 thro \ ugh 657)) selection = (chain 'C' and (resid 522 through 608 or resid 620 through 657)) selection = (chain 'D' and (resid 522 through 547 or resid 569 through 657)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'H' selection = (chain 'L' and resid 4 through 114) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 38.190 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.021 0.154 15130 Z= 1.117 Angle : 1.710 11.834 20667 Z= 1.098 Chirality : 0.124 0.510 2490 Planarity : 0.009 0.050 2577 Dihedral : 10.733 109.419 5996 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.60 (0.20), residues: 1619 helix: -0.07 (0.26), residues: 369 sheet: 1.26 (0.23), residues: 417 loop : 0.29 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.010 TRP A 69 HIS 0.015 0.002 HIS A 374 PHE 0.032 0.007 PHE E 376 TYR 0.041 0.007 TYR F 191 ARG 0.009 0.001 ARG C 542 Details of bonding type rmsd link_NAG-ASN : bond 0.07899 ( 33) link_NAG-ASN : angle 2.80298 ( 99) link_BETA1-4 : bond 0.07143 ( 9) link_BETA1-4 : angle 5.17536 ( 27) link_ALPHA1-3 : bond 0.08547 ( 1) link_ALPHA1-3 : angle 4.78192 ( 3) hydrogen bonds : bond 0.15691 ( 444) hydrogen bonds : angle 6.98809 ( 1167) SS BOND : bond 0.02083 ( 33) SS BOND : angle 3.21469 ( 66) covalent geometry : bond 0.02101 (15054) covalent geometry : angle 1.68533 (20472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8535 (m-80) cc_final: 0.8331 (m-80) REVERT: A 347 LYS cc_start: 0.8462 (tttt) cc_final: 0.8256 (ttmm) REVERT: A 434 MET cc_start: 0.9062 (ttp) cc_final: 0.8809 (ttm) REVERT: E 128 THR cc_start: 0.9024 (m) cc_final: 0.8816 (p) REVERT: E 138 ILE cc_start: 0.6305 (mm) cc_final: 0.6094 (mm) REVERT: E 274 SER cc_start: 0.8326 (t) cc_final: 0.8122 (p) REVERT: E 351 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7484 (ttmm) REVERT: E 500 ARG cc_start: 0.6413 (mmt180) cc_final: 0.5708 (mtt180) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.2881 time to fit residues: 195.8854 Evaluate side-chains 283 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 287 GLN A 425 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN C 630 GLN E 328 GLN E 352 HIS F 300 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.179716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.149782 restraints weight = 19821.584| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.54 r_work: 0.3540 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15130 Z= 0.165 Angle : 0.726 8.393 20667 Z= 0.361 Chirality : 0.046 0.186 2490 Planarity : 0.004 0.043 2577 Dihedral : 6.874 62.266 2873 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.90 % Allowed : 9.57 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1619 helix: 1.25 (0.28), residues: 355 sheet: 1.05 (0.24), residues: 407 loop : -0.27 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 479 HIS 0.006 0.001 HIS E 374 PHE 0.020 0.002 PHE F 353 TYR 0.023 0.002 TYR B 638 ARG 0.008 0.001 ARG F 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 33) link_NAG-ASN : angle 3.11475 ( 99) link_BETA1-4 : bond 0.00713 ( 9) link_BETA1-4 : angle 3.04535 ( 27) link_ALPHA1-3 : bond 0.01310 ( 1) link_ALPHA1-3 : angle 1.44864 ( 3) hydrogen bonds : bond 0.05322 ( 444) hydrogen bonds : angle 5.45922 ( 1167) SS BOND : bond 0.00376 ( 33) SS BOND : angle 1.17736 ( 66) covalent geometry : bond 0.00367 (15054) covalent geometry : angle 0.68457 (20472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 347 time to evaluate : 1.661 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 139 THR cc_start: 0.8633 (t) cc_final: 0.8288 (p) REVERT: A 153 MET cc_start: 0.8122 (ttm) cc_final: 0.7846 (ttm) REVERT: B 540 GLN cc_start: 0.4995 (mm-40) cc_final: 0.4662 (mm-40) REVERT: C 621 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7302 (mt-10) REVERT: C 651 ASN cc_start: 0.8785 (t0) cc_final: 0.8569 (t0) REVERT: E 114 GLN cc_start: 0.8361 (tt0) cc_final: 0.8024 (tt0) REVERT: E 153 MET cc_start: 0.8723 (tpp) cc_final: 0.7872 (tpp) REVERT: E 199 SER cc_start: 0.7998 (t) cc_final: 0.7729 (p) REVERT: E 238 PRO cc_start: 0.8298 (Cg_endo) cc_final: 0.7710 (Cg_exo) REVERT: E 500 ARG cc_start: 0.6469 (mmt180) cc_final: 0.5901 (mtt180) REVERT: F 153 MET cc_start: 0.7534 (ptp) cc_final: 0.6847 (ptt) outliers start: 28 outliers final: 20 residues processed: 365 average time/residue: 0.2850 time to fit residues: 152.4801 Evaluate side-chains 293 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 273 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 103 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 152 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 162 GLN E 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.182096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.153375 restraints weight = 19847.115| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.47 r_work: 0.3535 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15130 Z= 0.156 Angle : 0.637 8.845 20667 Z= 0.321 Chirality : 0.044 0.243 2490 Planarity : 0.003 0.044 2577 Dihedral : 5.849 46.987 2873 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.44 % Allowed : 11.81 % Favored : 85.74 % 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: 0.41 (0.21), residues: 1619 helix: 1.35 (0.29), residues: 360 sheet: 0.68 (0.24), residues: 410 loop : -0.36 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 623 HIS 0.006 0.001 HIS E 352 PHE 0.016 0.002 PHE A 53 TYR 0.019 0.001 TYR A 191 ARG 0.006 0.001 ARG E 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 33) link_NAG-ASN : angle 2.37352 ( 99) link_BETA1-4 : bond 0.00707 ( 9) link_BETA1-4 : angle 2.42947 ( 27) link_ALPHA1-3 : bond 0.01197 ( 1) link_ALPHA1-3 : angle 1.73145 ( 3) hydrogen bonds : bond 0.04679 ( 444) hydrogen bonds : angle 5.11685 ( 1167) SS BOND : bond 0.00342 ( 33) SS BOND : angle 1.24656 ( 66) covalent geometry : bond 0.00356 (15054) covalent geometry : angle 0.60783 (20472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 1.554 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 139 THR cc_start: 0.8582 (t) cc_final: 0.8195 (p) REVERT: A 153 MET cc_start: 0.8321 (ttm) cc_final: 0.8010 (ttm) REVERT: A 267 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7470 (mm-30) REVERT: E 114 GLN cc_start: 0.8486 (tt0) cc_final: 0.8002 (tt0) REVERT: E 153 MET cc_start: 0.8780 (tpp) cc_final: 0.7899 (tpp) REVERT: E 233 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.5121 (p90) REVERT: E 500 ARG cc_start: 0.6667 (mmt180) cc_final: 0.5953 (mtt180) REVERT: D 585 ARG cc_start: 0.8949 (mmm-85) cc_final: 0.8727 (mmm-85) REVERT: F 153 MET cc_start: 0.7427 (ptp) cc_final: 0.6653 (ptt) REVERT: F 475 MET cc_start: 0.8821 (mmt) cc_final: 0.8569 (mmt) REVERT: F 490 LYS cc_start: 0.8908 (tttm) cc_final: 0.8682 (tttp) outliers start: 36 outliers final: 23 residues processed: 316 average time/residue: 0.2808 time to fit residues: 130.2452 Evaluate side-chains 284 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 48 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 374 HIS A 422 GLN B 540 GLN E 99 ASN E 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.170072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.141502 restraints weight = 20026.653| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.28 r_work: 0.3410 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15130 Z= 0.275 Angle : 0.771 9.622 20667 Z= 0.383 Chirality : 0.049 0.208 2490 Planarity : 0.005 0.062 2577 Dihedral : 6.464 50.635 2873 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.28 % Allowed : 11.00 % Favored : 84.73 % 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: -0.26 (0.20), residues: 1619 helix: 0.75 (0.28), residues: 375 sheet: 0.18 (0.23), residues: 428 loop : -0.76 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 479 HIS 0.008 0.002 HIS A 105 PHE 0.025 0.003 PHE A 376 TYR 0.020 0.002 TYR A 191 ARG 0.009 0.001 ARG E 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 33) link_NAG-ASN : angle 2.37995 ( 99) link_BETA1-4 : bond 0.00418 ( 9) link_BETA1-4 : angle 2.46949 ( 27) link_ALPHA1-3 : bond 0.00692 ( 1) link_ALPHA1-3 : angle 2.41669 ( 3) hydrogen bonds : bond 0.05285 ( 444) hydrogen bonds : angle 5.33024 ( 1167) SS BOND : bond 0.00600 ( 33) SS BOND : angle 1.14326 ( 66) covalent geometry : bond 0.00643 (15054) covalent geometry : angle 0.74764 (20472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 290 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8619 (t) cc_final: 0.8226 (p) REVERT: A 142 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8000 (mmt) REVERT: A 153 MET cc_start: 0.8409 (ttm) cc_final: 0.8088 (ttm) REVERT: A 267 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7923 (tp30) REVERT: A 499 THR cc_start: 0.8548 (m) cc_final: 0.8326 (p) REVERT: C 540 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: C 634 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8382 (mt-10) REVERT: E 85 HIS cc_start: 0.8739 (t70) cc_final: 0.8424 (t-170) REVERT: E 156 GLU cc_start: 0.7759 (mp0) cc_final: 0.7058 (mt-10) REVERT: E 233 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6883 (p90) REVERT: D 543 ASN cc_start: 0.8518 (m-40) cc_final: 0.8102 (m110) REVERT: D 579 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7254 (mtp85) REVERT: F 153 MET cc_start: 0.7404 (ptp) cc_final: 0.6884 (ptt) REVERT: F 490 LYS cc_start: 0.8901 (tttm) cc_final: 0.8600 (tttp) outliers start: 63 outliers final: 43 residues processed: 331 average time/residue: 0.2833 time to fit residues: 137.0369 Evaluate side-chains 320 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 149 CYS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 77 optimal weight: 0.0870 chunk 24 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 134 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN E 103 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.171765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144327 restraints weight = 20229.456| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.21 r_work: 0.3443 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15130 Z= 0.128 Angle : 0.592 8.184 20667 Z= 0.295 Chirality : 0.043 0.197 2490 Planarity : 0.003 0.046 2577 Dihedral : 5.711 52.254 2873 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.51 % Allowed : 14.05 % Favored : 83.44 % 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: -0.06 (0.20), residues: 1619 helix: 1.00 (0.28), residues: 375 sheet: 0.31 (0.24), residues: 414 loop : -0.67 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 623 HIS 0.007 0.001 HIS E 374 PHE 0.014 0.001 PHE A 376 TYR 0.024 0.002 TYR A 165 ARG 0.006 0.001 ARG E 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 33) link_NAG-ASN : angle 2.05644 ( 99) link_BETA1-4 : bond 0.00485 ( 9) link_BETA1-4 : angle 1.89275 ( 27) link_ALPHA1-3 : bond 0.01163 ( 1) link_ALPHA1-3 : angle 2.16065 ( 3) hydrogen bonds : bond 0.04127 ( 444) hydrogen bonds : angle 4.95763 ( 1167) SS BOND : bond 0.00352 ( 33) SS BOND : angle 0.77091 ( 66) covalent geometry : bond 0.00290 (15054) covalent geometry : angle 0.57148 (20472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 293 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8695 (t) cc_final: 0.8385 (p) REVERT: A 153 MET cc_start: 0.8291 (ttm) cc_final: 0.7994 (ttm) REVERT: A 190 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8024 (mp0) REVERT: A 265 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8822 (mp) REVERT: A 267 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7800 (tp30) REVERT: A 280 ASN cc_start: 0.8345 (m-40) cc_final: 0.8111 (m110) REVERT: A 500 ARG cc_start: 0.6191 (ttt-90) cc_final: 0.5616 (ttt-90) REVERT: C 540 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.6683 (mp10) REVERT: C 634 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8373 (mt-10) REVERT: E 85 HIS cc_start: 0.8639 (t70) cc_final: 0.8338 (t-170) REVERT: E 114 GLN cc_start: 0.8484 (tt0) cc_final: 0.8164 (tt0) REVERT: E 156 GLU cc_start: 0.7721 (mp0) cc_final: 0.7167 (mt-10) REVERT: E 233 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.5713 (p90) REVERT: F 486 TYR cc_start: 0.8953 (m-80) cc_final: 0.8422 (m-10) REVERT: F 490 LYS cc_start: 0.8865 (tttm) cc_final: 0.8615 (tttp) outliers start: 37 outliers final: 25 residues processed: 318 average time/residue: 0.2643 time to fit residues: 122.8606 Evaluate side-chains 309 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 281 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.166456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138519 restraints weight = 20307.757| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.27 r_work: 0.3374 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 15130 Z= 0.343 Angle : 0.820 9.991 20667 Z= 0.401 Chirality : 0.051 0.226 2490 Planarity : 0.004 0.050 2577 Dihedral : 6.777 52.795 2873 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.41 % Allowed : 13.44 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1619 helix: 0.62 (0.28), residues: 366 sheet: -0.15 (0.25), residues: 401 loop : -0.95 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 316 HIS 0.009 0.002 HIS E 374 PHE 0.029 0.003 PHE A 376 TYR 0.019 0.003 TYR A 165 ARG 0.007 0.001 ARG F 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 33) link_NAG-ASN : angle 2.41527 ( 99) link_BETA1-4 : bond 0.00394 ( 9) link_BETA1-4 : angle 2.51709 ( 27) link_ALPHA1-3 : bond 0.00888 ( 1) link_ALPHA1-3 : angle 2.63579 ( 3) hydrogen bonds : bond 0.05527 ( 444) hydrogen bonds : angle 5.36744 ( 1167) SS BOND : bond 0.00593 ( 33) SS BOND : angle 1.42946 ( 66) covalent geometry : bond 0.00818 (15054) covalent geometry : angle 0.79674 (20472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 296 time to evaluate : 1.492 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 116 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8565 (mp) REVERT: A 139 THR cc_start: 0.8683 (t) cc_final: 0.8345 (p) REVERT: A 142 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8057 (mtp) REVERT: A 153 MET cc_start: 0.8365 (ttm) cc_final: 0.8033 (ttm) REVERT: A 189 LYS cc_start: 0.7934 (mttt) cc_final: 0.7708 (mtmt) REVERT: A 265 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 342 LEU cc_start: 0.9291 (tp) cc_final: 0.9086 (tp) REVERT: C 540 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.6644 (mp10) REVERT: C 634 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8399 (mt-10) REVERT: E 156 GLU cc_start: 0.7940 (mp0) cc_final: 0.7396 (mt-10) REVERT: E 233 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6621 (p90) REVERT: D 543 ASN cc_start: 0.8531 (m-40) cc_final: 0.8121 (m110) REVERT: D 579 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7329 (mtp85) REVERT: F 153 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6822 (ptt) REVERT: F 160 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7681 (tptp) REVERT: F 486 TYR cc_start: 0.9040 (m-80) cc_final: 0.8750 (m-10) REVERT: F 490 LYS cc_start: 0.8919 (tttm) cc_final: 0.8589 (tttp) outliers start: 65 outliers final: 48 residues processed: 336 average time/residue: 0.2784 time to fit residues: 135.2689 Evaluate side-chains 337 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 149 CYS Chi-restraints excluded: chain F residue 153 MET Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 153 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN E 348 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.170713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.140801 restraints weight = 20147.196| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.51 r_work: 0.3429 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15130 Z= 0.136 Angle : 0.610 8.413 20667 Z= 0.304 Chirality : 0.043 0.198 2490 Planarity : 0.004 0.048 2577 Dihedral : 5.998 57.812 2873 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.05 % Allowed : 15.95 % Favored : 80.99 % 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: -0.41 (0.20), residues: 1619 helix: 0.82 (0.28), residues: 376 sheet: 0.00 (0.25), residues: 413 loop : -0.90 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 338 HIS 0.006 0.001 HIS E 374 PHE 0.015 0.001 PHE A 376 TYR 0.019 0.001 TYR A 165 ARG 0.011 0.001 ARG C 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 33) link_NAG-ASN : angle 2.10474 ( 99) link_BETA1-4 : bond 0.00475 ( 9) link_BETA1-4 : angle 1.87229 ( 27) link_ALPHA1-3 : bond 0.01161 ( 1) link_ALPHA1-3 : angle 2.20932 ( 3) hydrogen bonds : bond 0.04208 ( 444) hydrogen bonds : angle 4.97295 ( 1167) SS BOND : bond 0.00338 ( 33) SS BOND : angle 1.02876 ( 66) covalent geometry : bond 0.00313 (15054) covalent geometry : angle 0.58765 (20472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 304 time to evaluate : 1.710 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 139 THR cc_start: 0.8606 (t) cc_final: 0.8343 (p) REVERT: A 153 MET cc_start: 0.7995 (ttm) cc_final: 0.7665 (ttm) REVERT: A 265 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8780 (mp) REVERT: A 342 LEU cc_start: 0.9156 (tp) cc_final: 0.8954 (tp) REVERT: A 500 ARG cc_start: 0.6080 (ttt-90) cc_final: 0.5647 (ttt-90) REVERT: B 626 MET cc_start: 0.8040 (ttm) cc_final: 0.7817 (ttm) REVERT: C 634 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8222 (mt-10) REVERT: E 114 GLN cc_start: 0.8379 (tt0) cc_final: 0.8072 (tt0) REVERT: E 156 GLU cc_start: 0.7634 (mp0) cc_final: 0.7159 (mt-10) REVERT: E 157 LEU cc_start: 0.8164 (mt) cc_final: 0.7916 (mp) REVERT: E 233 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.5959 (p90) REVERT: E 475 MET cc_start: 0.7895 (mmt) cc_final: 0.7560 (mmt) REVERT: D 543 ASN cc_start: 0.8224 (m-40) cc_final: 0.7872 (m110) REVERT: D 579 ARG cc_start: 0.7808 (mtp180) cc_final: 0.7160 (mtt90) REVERT: D 585 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8499 (mtm-85) REVERT: F 46 LYS cc_start: 0.9081 (mttm) cc_final: 0.8869 (mmtt) REVERT: F 160 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7602 (tptp) REVERT: F 316 TRP cc_start: 0.7986 (m100) cc_final: 0.7033 (m100) REVERT: F 360 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7497 (ttp80) REVERT: F 486 TYR cc_start: 0.8934 (m-80) cc_final: 0.8293 (m-10) REVERT: F 490 LYS cc_start: 0.8789 (tttm) cc_final: 0.8466 (tttp) outliers start: 45 outliers final: 33 residues processed: 335 average time/residue: 0.2813 time to fit residues: 138.5354 Evaluate side-chains 322 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 149 CYS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 151 optimal weight: 0.0000 chunk 77 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.171730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.141682 restraints weight = 20039.345| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.53 r_work: 0.3441 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15130 Z= 0.116 Angle : 0.589 9.094 20667 Z= 0.294 Chirality : 0.043 0.197 2490 Planarity : 0.003 0.045 2577 Dihedral : 5.723 59.734 2873 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.51 % Allowed : 16.56 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.25 (0.21), residues: 1619 helix: 1.04 (0.28), residues: 370 sheet: 0.07 (0.24), residues: 428 loop : -0.82 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 338 HIS 0.006 0.001 HIS E 374 PHE 0.014 0.001 PHE A 376 TYR 0.022 0.001 TYR A 165 ARG 0.007 0.001 ARG E 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 33) link_NAG-ASN : angle 1.95891 ( 99) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 1.74591 ( 27) link_ALPHA1-3 : bond 0.00993 ( 1) link_ALPHA1-3 : angle 1.79044 ( 3) hydrogen bonds : bond 0.03970 ( 444) hydrogen bonds : angle 4.85015 ( 1167) SS BOND : bond 0.00300 ( 33) SS BOND : angle 1.43586 ( 66) covalent geometry : bond 0.00268 (15054) covalent geometry : angle 0.56665 (20472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7973 (ttm) cc_final: 0.7632 (ttm) REVERT: A 170 ARG cc_start: 0.8569 (tpt90) cc_final: 0.8313 (tpt90) REVERT: A 265 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8736 (mp) REVERT: A 280 ASN cc_start: 0.8269 (m-40) cc_final: 0.8066 (m110) REVERT: A 500 ARG cc_start: 0.6008 (ttt-90) cc_final: 0.5667 (ttt-90) REVERT: C 540 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.6610 (mp10) REVERT: C 634 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8247 (mt-10) REVERT: E 114 GLN cc_start: 0.8357 (tt0) cc_final: 0.8065 (tt0) REVERT: E 157 LEU cc_start: 0.8129 (mt) cc_final: 0.7881 (mp) REVERT: E 199 SER cc_start: 0.7484 (t) cc_final: 0.7260 (p) REVERT: E 233 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.5882 (p90) REVERT: E 475 MET cc_start: 0.7848 (mmt) cc_final: 0.7554 (mmt) REVERT: D 543 ASN cc_start: 0.8234 (m-40) cc_final: 0.7897 (m110) REVERT: F 160 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7585 (tptp) REVERT: F 486 TYR cc_start: 0.8912 (m-80) cc_final: 0.8321 (m-10) REVERT: F 490 LYS cc_start: 0.8814 (tttm) cc_final: 0.8505 (tttp) outliers start: 37 outliers final: 26 residues processed: 316 average time/residue: 0.2986 time to fit residues: 138.0058 Evaluate side-chains 312 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 159 optimal weight: 0.8980 chunk 155 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 157 optimal weight: 0.2980 chunk 177 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 101 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.176829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.147275 restraints weight = 19851.172| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.49 r_work: 0.3389 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15130 Z= 0.105 Angle : 0.576 9.789 20667 Z= 0.288 Chirality : 0.042 0.186 2490 Planarity : 0.003 0.051 2577 Dihedral : 5.339 53.539 2873 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.70 % Allowed : 17.24 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.14 (0.21), residues: 1619 helix: 1.11 (0.28), residues: 374 sheet: 0.24 (0.25), residues: 423 loop : -0.81 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 631 HIS 0.005 0.001 HIS E 374 PHE 0.010 0.001 PHE A 376 TYR 0.022 0.001 TYR A 165 ARG 0.007 0.001 ARG C 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 33) link_NAG-ASN : angle 1.79492 ( 99) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 1.57239 ( 27) link_ALPHA1-3 : bond 0.00862 ( 1) link_ALPHA1-3 : angle 1.56416 ( 3) hydrogen bonds : bond 0.03661 ( 444) hydrogen bonds : angle 4.76442 ( 1167) SS BOND : bond 0.00259 ( 33) SS BOND : angle 1.47415 ( 66) covalent geometry : bond 0.00237 (15054) covalent geometry : angle 0.55524 (20472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 294 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8010 (ttm) cc_final: 0.7679 (ttm) REVERT: A 265 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 280 ASN cc_start: 0.8198 (m-40) cc_final: 0.7959 (m110) REVERT: A 500 ARG cc_start: 0.6093 (ttt-90) cc_final: 0.5882 (ttt-90) REVERT: C 540 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.6690 (mp10) REVERT: C 588 ARG cc_start: 0.7098 (mtt180) cc_final: 0.6194 (tmm-80) REVERT: C 634 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8368 (mt-10) REVERT: E 114 GLN cc_start: 0.8344 (tt0) cc_final: 0.8063 (tt0) REVERT: E 156 GLU cc_start: 0.7704 (mp0) cc_final: 0.6776 (mt-10) REVERT: E 233 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.5917 (p90) REVERT: E 475 MET cc_start: 0.7811 (mmt) cc_final: 0.7526 (mmt) REVERT: D 543 ASN cc_start: 0.8164 (m-40) cc_final: 0.7868 (m-40) REVERT: F 160 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7582 (tptp) REVERT: F 316 TRP cc_start: 0.8112 (m100) cc_final: 0.7790 (m100) REVERT: F 486 TYR cc_start: 0.8840 (m-80) cc_final: 0.8188 (m-10) REVERT: F 490 LYS cc_start: 0.8794 (tttm) cc_final: 0.8514 (tttp) outliers start: 25 outliers final: 20 residues processed: 311 average time/residue: 0.3187 time to fit residues: 143.7023 Evaluate side-chains 297 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.169701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141364 restraints weight = 20339.429| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.29 r_work: 0.3401 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 15130 Z= 0.255 Angle : 0.729 12.359 20667 Z= 0.358 Chirality : 0.047 0.214 2490 Planarity : 0.004 0.053 2577 Dihedral : 6.010 46.274 2873 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.38 % Allowed : 16.84 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.13 % 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: -0.37 (0.21), residues: 1619 helix: 0.90 (0.28), residues: 367 sheet: -0.05 (0.26), residues: 393 loop : -0.82 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 631 HIS 0.005 0.002 HIS E 374 PHE 0.028 0.002 PHE A 376 TYR 0.026 0.002 TYR E 486 ARG 0.007 0.001 ARG A 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 33) link_NAG-ASN : angle 2.09392 ( 99) link_BETA1-4 : bond 0.00398 ( 9) link_BETA1-4 : angle 2.10331 ( 27) link_ALPHA1-3 : bond 0.00768 ( 1) link_ALPHA1-3 : angle 2.05695 ( 3) hydrogen bonds : bond 0.04772 ( 444) hydrogen bonds : angle 5.08085 ( 1167) SS BOND : bond 0.00502 ( 33) SS BOND : angle 1.98655 ( 66) covalent geometry : bond 0.00610 (15054) covalent geometry : angle 0.70398 (20472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8699 (mmm) cc_final: 0.7643 (mmt) REVERT: A 153 MET cc_start: 0.8276 (ttm) cc_final: 0.7973 (ttm) REVERT: A 265 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8795 (mp) REVERT: A 500 ARG cc_start: 0.6049 (ttt-90) cc_final: 0.5680 (ttt-90) REVERT: C 540 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.6813 (mp10) REVERT: C 634 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8357 (mt-10) REVERT: E 156 GLU cc_start: 0.7896 (mp0) cc_final: 0.6983 (mt-10) REVERT: E 233 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6127 (p90) REVERT: D 543 ASN cc_start: 0.8357 (m-40) cc_final: 0.7981 (m110) REVERT: D 579 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7241 (mtp85) REVERT: F 160 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7587 (tptp) REVERT: F 316 TRP cc_start: 0.8215 (m100) cc_final: 0.7872 (m100) REVERT: F 490 LYS cc_start: 0.8929 (tttm) cc_final: 0.8623 (tttp) outliers start: 35 outliers final: 28 residues processed: 294 average time/residue: 0.2923 time to fit residues: 125.5828 Evaluate side-chains 303 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 57 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.170259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139988 restraints weight = 20157.516| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.53 r_work: 0.3401 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15130 Z= 0.159 Angle : 0.639 10.735 20667 Z= 0.317 Chirality : 0.044 0.196 2490 Planarity : 0.004 0.056 2577 Dihedral : 5.685 44.882 2873 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.04 % Allowed : 17.31 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.13 % 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: -0.34 (0.21), residues: 1619 helix: 0.91 (0.28), residues: 373 sheet: -0.04 (0.26), residues: 398 loop : -0.80 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 631 HIS 0.006 0.001 HIS E 374 PHE 0.023 0.002 PHE A 53 TYR 0.023 0.002 TYR A 165 ARG 0.008 0.001 ARG C 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 33) link_NAG-ASN : angle 1.99958 ( 99) link_BETA1-4 : bond 0.00412 ( 9) link_BETA1-4 : angle 1.82804 ( 27) link_ALPHA1-3 : bond 0.00828 ( 1) link_ALPHA1-3 : angle 1.87171 ( 3) hydrogen bonds : bond 0.04187 ( 444) hydrogen bonds : angle 4.93217 ( 1167) SS BOND : bond 0.00373 ( 33) SS BOND : angle 1.71977 ( 66) covalent geometry : bond 0.00376 (15054) covalent geometry : angle 0.61541 (20472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8201.74 seconds wall clock time: 144 minutes 57.23 seconds (8697.23 seconds total)