Starting phenix.real_space_refine on Fri May 16 18:27:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sww_40823/05_2025/8sww_40823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sww_40823/05_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_40823/05_2025/8sww_40823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sww_40823/05_2025/8sww_40823.map" model { file = "/net/cci-nas-00/data/ceres_data/8sww_40823/05_2025/8sww_40823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sww_40823/05_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-5687/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: 9.20, per 1000 atoms: 0.62 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: 4.14 Conformation dependent library (CDL) restraints added in 1.6 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: 1.79 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: 4.34 Time building geometry restraints manager: 4.75 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: 1.910 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.150 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- 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 : 1.432 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: 0.2880 time to fit residues: 196.9006 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 : 1.467 ------------------------------------------------------------------------------- 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 = 0.149781 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 : 1.500 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: 0.8287 (p) REVERT: A 153 MET cc_start: 0.8121 (ttm) cc_final: 0.7845 (ttm) REVERT: B 540 GLN cc_start: 0.4993 (mm-40) cc_final: 0.4662 (mm-40) REVERT: C 621 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7305 (mt-10) REVERT: C 651 ASN cc_start: 0.8783 (t0) cc_final: 0.8567 (t0) REVERT: E 114 GLN cc_start: 0.8360 (tt0) cc_final: 0.8023 (tt0) REVERT: E 153 MET cc_start: 0.8721 (tpp) cc_final: 0.7872 (tpp) REVERT: E 199 SER cc_start: 0.7997 (t) cc_final: 0.7729 (p) REVERT: E 238 PRO cc_start: 0.8297 (Cg_endo) cc_final: 0.7713 (Cg_exo) REVERT: E 500 ARG cc_start: 0.6470 (mmt180) cc_final: 0.5901 (mtt180) REVERT: F 153 MET cc_start: 0.7536 (ptp) cc_final: 0.6850 (ptt) outliers start: 28 outliers final: 20 residues processed: 365 average time/residue: 0.2708 time to fit residues: 143.5806 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 : 1.444 ------------------------------------------------------------------------------- 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: 2.9990 chunk 138 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 152 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4008 r_free = 0.4008 target = 0.182363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.153640 restraints weight = 19837.723| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.47 r_work: 0.3538 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15130 Z= 0.152 Angle : 0.636 8.955 20667 Z= 0.320 Chirality : 0.044 0.249 2490 Planarity : 0.003 0.043 2577 Dihedral : 5.830 46.910 2873 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.94 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: 0.42 (0.21), residues: 1619 helix: 1.36 (0.29), residues: 360 sheet: 0.68 (0.24), residues: 410 loop : -0.35 (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 0.018 0.001 TYR A 191 ARG 0.006 0.001 ARG E 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 33) link_NAG-ASN : angle 2.36689 ( 99) link_BETA1-4 : bond 0.00685 ( 9) link_BETA1-4 : angle 2.41919 ( 27) link_ALPHA1-3 : bond 0.01189 ( 1) link_ALPHA1-3 : angle 1.71261 ( 3) hydrogen bonds : bond 0.04668 ( 444) hydrogen bonds : angle 5.11794 ( 1167) SS BOND : bond 0.00371 ( 33) SS BOND : angle 1.20384 ( 66) covalent geometry : bond 0.00344 (15054) covalent geometry : angle 0.60669 (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 330 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 294 time to evaluate : 1.453 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: 0.8577 (t) cc_final: 0.8192 (p) REVERT: A 153 MET cc_start: 0.8334 (ttm) cc_final: 0.8027 (ttm) REVERT: A 267 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7460 (mm-30) REVERT: E 114 GLN cc_start: 0.8478 (tt0) cc_final: 0.7998 (tt0) REVERT: E 153 MET cc_start: 0.8777 (tpp) cc_final: 0.7875 (tpp) REVERT: E 233 PHE cc_start: 0.6451 (OUTLIER) cc_final: 0.5117 (p90) REVERT: E 500 ARG cc_start: 0.6661 (mmt180) cc_final: 0.5986 (mtt180) REVERT: D 585 ARG cc_start: 0.8943 (mmm-85) cc_final: 0.8720 (mmm-85) REVERT: F 153 MET cc_start: 0.7424 (ptp) cc_final: 0.6655 (ptt) REVERT: F 475 MET cc_start: 0.8820 (mmt) cc_final: 0.8563 (mmt) REVERT: F 490 LYS cc_start: 0.8905 (tttm) cc_final: 0.8678 (tttp) outliers start: 36 outliers final: 23 residues processed: 318 average time/residue: 0.2547 time to fit residues: 118.6033 Evaluate side-chains 286 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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: 0.8980 chunk 158 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 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: 2.3788 ------------------------------------------------------------------------------- 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 B 540 GLN E 99 ASN E 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.170016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141378 restraints weight = 20019.235| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.29 r_work: 0.3403 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 15130 Z= 0.278 Angle : 0.775 9.794 20667 Z= 0.385 Chirality : 0.049 0.205 2490 Planarity : 0.005 0.054 2577 Dihedral : 6.416 49.375 2873 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.41 % Allowed : 10.79 % Favored : 84.79 % 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: 0.20 (0.23), residues: 428 loop : -0.77 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 479 HIS 0.009 0.002 HIS A 105 PHE 0.025 0.003 PHE A 376 TYR 0.018 0.002 TYR A 191 ARG 0.011 0.001 ARG C 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 33) link_NAG-ASN : angle 2.38283 ( 99) link_BETA1-4 : bond 0.00420 ( 9) link_BETA1-4 : angle 2.47607 ( 27) link_ALPHA1-3 : bond 0.00997 ( 1) link_ALPHA1-3 : angle 2.64148 ( 3) hydrogen bonds : bond 0.05270 ( 444) hydrogen bonds : angle 5.31693 ( 1167) SS BOND : bond 0.00777 ( 33) SS BOND : angle 1.20921 ( 66) covalent geometry : bond 0.00651 (15054) covalent geometry : angle 0.75218 (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 356 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 1.816 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: 0.8660 (t) cc_final: 0.8276 (p) REVERT: A 142 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8001 (mmt) REVERT: A 153 MET cc_start: 0.8455 (ttm) cc_final: 0.8146 (ttm) REVERT: A 267 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7960 (tp30) REVERT: A 499 THR cc_start: 0.8531 (m) cc_final: 0.8305 (p) REVERT: C 540 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: E 85 HIS cc_start: 0.8730 (t70) cc_final: 0.8382 (t-170) REVERT: E 156 GLU cc_start: 0.7813 (mp0) cc_final: 0.7139 (mt-10) REVERT: E 233 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6854 (p90) REVERT: E 292 VAL cc_start: 0.8659 (t) cc_final: 0.8275 (m) REVERT: D 543 ASN cc_start: 0.8522 (m-40) cc_final: 0.8106 (m110) REVERT: D 579 ARG cc_start: 0.8024 (mtp180) cc_final: 0.7261 (mtp85) REVERT: F 153 MET cc_start: 0.7402 (ptp) cc_final: 0.6879 (ptt) REVERT: F 490 LYS cc_start: 0.8911 (tttm) cc_final: 0.8602 (tttp) outliers start: 65 outliers final: 45 residues processed: 334 average time/residue: 0.2665 time to fit residues: 129.7920 Evaluate side-chains 319 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 271 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 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 236 THR 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 388 SER 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 501 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 77 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.170764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143409 restraints weight = 20279.665| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.20 r_work: 0.3434 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15130 Z= 0.149 Angle : 0.616 8.580 20667 Z= 0.305 Chirality : 0.044 0.200 2490 Planarity : 0.003 0.048 2577 Dihedral : 5.856 52.998 2873 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.65 % Allowed : 13.92 % Favored : 83.44 % 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: -0.10 (0.20), residues: 1619 helix: 1.05 (0.28), residues: 369 sheet: 0.25 (0.24), residues: 414 loop : -0.70 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 631 HIS 0.008 0.001 HIS E 374 PHE 0.017 0.002 PHE A 376 TYR 0.026 0.002 TYR A 165 ARG 0.005 0.001 ARG E 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 33) link_NAG-ASN : angle 2.10456 ( 99) link_BETA1-4 : bond 0.00468 ( 9) link_BETA1-4 : angle 1.99545 ( 27) link_ALPHA1-3 : bond 0.01034 ( 1) link_ALPHA1-3 : angle 2.25505 ( 3) hydrogen bonds : bond 0.04313 ( 444) hydrogen bonds : angle 5.00683 ( 1167) SS BOND : bond 0.00394 ( 33) SS BOND : angle 0.96839 ( 66) covalent geometry : bond 0.00345 (15054) covalent geometry : angle 0.59353 (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 337 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8710 (t) cc_final: 0.8393 (p) REVERT: A 153 MET cc_start: 0.8321 (ttm) cc_final: 0.8013 (ttm) REVERT: A 190 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8012 (mp0) REVERT: A 231 LYS cc_start: 0.8191 (mmtp) cc_final: 0.7941 (mmtp) REVERT: A 265 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8801 (mp) REVERT: A 302 ASN cc_start: 0.8983 (m-40) cc_final: 0.8762 (t0) REVERT: A 500 ARG cc_start: 0.6287 (ttt-90) cc_final: 0.5702 (ttt-90) REVERT: C 540 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: C 634 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8471 (mt-10) REVERT: E 85 HIS cc_start: 0.8632 (t70) cc_final: 0.8338 (t-170) REVERT: E 114 GLN cc_start: 0.8506 (tt0) cc_final: 0.8189 (tt0) REVERT: E 156 GLU cc_start: 0.7756 (mp0) cc_final: 0.7189 (mt-10) REVERT: E 233 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.5807 (p90) REVERT: E 292 VAL cc_start: 0.8624 (t) cc_final: 0.8279 (m) REVERT: E 484 TYR cc_start: 0.8731 (p90) cc_final: 0.8516 (p90) REVERT: D 585 ARG cc_start: 0.8994 (mmm-85) cc_final: 0.8694 (mtm-85) REVERT: F 486 TYR cc_start: 0.8972 (m-80) cc_final: 0.8425 (m-10) REVERT: F 490 LYS cc_start: 0.8880 (tttm) cc_final: 0.8627 (tttp) outliers start: 39 outliers final: 27 residues processed: 326 average time/residue: 0.2605 time to fit residues: 124.6935 Evaluate side-chains 319 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN 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 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 243 SER Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain D residue 591 GLN 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 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 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: 3.9990 chunk 149 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 47 optimal weight: 0.0040 chunk 94 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 overall best weight: 2.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN E 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.164333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135294 restraints weight = 20286.110| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.32 r_work: 0.3367 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15130 Z= 0.258 Angle : 0.727 9.356 20667 Z= 0.358 Chirality : 0.048 0.216 2490 Planarity : 0.004 0.059 2577 Dihedral : 6.378 56.089 2873 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.87 % Allowed : 13.92 % Favored : 82.21 % 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: 0.84 (0.28), residues: 367 sheet: -0.04 (0.25), residues: 399 loop : -0.85 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 631 HIS 0.009 0.002 HIS E 374 PHE 0.024 0.002 PHE A 376 TYR 0.019 0.002 TYR A 165 ARG 0.010 0.001 ARG C 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 33) link_NAG-ASN : angle 2.26733 ( 99) link_BETA1-4 : bond 0.00438 ( 9) link_BETA1-4 : angle 2.29068 ( 27) link_ALPHA1-3 : bond 0.00882 ( 1) link_ALPHA1-3 : angle 2.42785 ( 3) hydrogen bonds : bond 0.05025 ( 444) hydrogen bonds : angle 5.17422 ( 1167) SS BOND : bond 0.00488 ( 33) SS BOND : angle 1.13091 ( 66) covalent geometry : bond 0.00612 (15054) covalent geometry : angle 0.70527 (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 343 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8341 (tm-30) REVERT: A 116 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8541 (mp) REVERT: A 139 THR cc_start: 0.8687 (t) cc_final: 0.8346 (p) REVERT: A 142 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7989 (mtp) REVERT: A 153 MET cc_start: 0.8427 (ttm) cc_final: 0.8121 (ttm) REVERT: A 189 LYS cc_start: 0.7852 (mttt) cc_final: 0.7604 (mtmt) REVERT: A 265 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8852 (mp) REVERT: A 342 LEU cc_start: 0.9297 (tp) cc_final: 0.9073 (tp) REVERT: C 540 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.6563 (mp10) REVERT: C 634 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8480 (mt-10) REVERT: E 156 GLU cc_start: 0.7901 (mp0) cc_final: 0.7359 (mt-10) REVERT: E 233 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6561 (p90) REVERT: D 543 ASN cc_start: 0.8409 (m-40) cc_final: 0.7967 (m110) REVERT: D 579 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7254 (mtp85) REVERT: D 585 ARG cc_start: 0.9054 (mmm-85) cc_final: 0.8685 (mtm-85) REVERT: F 316 TRP cc_start: 0.8197 (m100) cc_final: 0.7792 (m100) REVERT: F 490 LYS cc_start: 0.8901 (tttm) cc_final: 0.8566 (tttp) outliers start: 57 outliers final: 43 residues processed: 324 average time/residue: 0.2767 time to fit residues: 131.0048 Evaluate side-chains 321 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 138 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 209 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 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 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 342 LEU 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 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: 3.9990 chunk 62 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.170105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142535 restraints weight = 20381.603| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.22 r_work: 0.3399 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4398 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= 0.141 Angle : 0.611 8.454 20667 Z= 0.305 Chirality : 0.044 0.199 2490 Planarity : 0.003 0.048 2577 Dihedral : 5.950 54.293 2873 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.99 % Allowed : 15.48 % Favored : 81.53 % 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: -0.27 (0.20), residues: 1619 helix: 0.99 (0.28), residues: 369 sheet: 0.16 (0.25), residues: 407 loop : -0.86 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 631 HIS 0.006 0.001 HIS E 374 PHE 0.016 0.001 PHE A 376 TYR 0.018 0.001 TYR A 165 ARG 0.009 0.001 ARG E 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 33) link_NAG-ASN : angle 2.08663 ( 99) link_BETA1-4 : bond 0.00428 ( 9) link_BETA1-4 : angle 1.89108 ( 27) link_ALPHA1-3 : bond 0.00992 ( 1) link_ALPHA1-3 : angle 2.07353 ( 3) hydrogen bonds : bond 0.04239 ( 444) hydrogen bonds : angle 4.91809 ( 1167) SS BOND : bond 0.00355 ( 33) SS BOND : angle 1.29907 ( 66) covalent geometry : bond 0.00326 (15054) covalent geometry : angle 0.58714 (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 338 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8292 (tm-30) REVERT: A 139 THR cc_start: 0.8686 (t) cc_final: 0.8408 (p) REVERT: A 153 MET cc_start: 0.8293 (ttm) cc_final: 0.7982 (ttm) REVERT: A 265 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8816 (mp) REVERT: A 342 LEU cc_start: 0.9184 (tp) cc_final: 0.8980 (tp) REVERT: A 499 THR cc_start: 0.8314 (m) cc_final: 0.8038 (p) REVERT: A 500 ARG cc_start: 0.6224 (ttt-90) cc_final: 0.5719 (ttt-90) REVERT: C 540 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.6639 (mp10) REVERT: C 634 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8400 (mt-10) REVERT: E 156 GLU cc_start: 0.7772 (mp0) cc_final: 0.7292 (mt-10) REVERT: E 233 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6026 (p90) REVERT: E 475 MET cc_start: 0.8063 (mmt) cc_final: 0.7673 (mmt) REVERT: D 543 ASN cc_start: 0.8301 (m-40) cc_final: 0.7961 (m110) REVERT: D 579 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7233 (mtp85) REVERT: D 585 ARG cc_start: 0.9025 (mmm-85) cc_final: 0.8698 (mtm-85) REVERT: F 316 TRP cc_start: 0.8135 (m100) cc_final: 0.7217 (m100) REVERT: F 490 LYS cc_start: 0.8859 (tttm) cc_final: 0.8567 (tttp) outliers start: 44 outliers final: 33 residues processed: 325 average time/residue: 0.2564 time to fit residues: 121.6488 Evaluate side-chains 314 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 340 GLU Chi-restraints excluded: chain A residue 346 VAL 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 B residue 649 SER 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 145 GLU 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 243 SER Chi-restraints excluded: chain E residue 292 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 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 240 THR 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 439 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 496 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: 0.9980 chunk 77 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 0.1980 chunk 103 optimal weight: 0.0770 chunk 126 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.175318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146238 restraints weight = 20123.876| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.46 r_work: 0.3465 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15130 Z= 0.112 Angle : 0.575 8.608 20667 Z= 0.288 Chirality : 0.043 0.192 2490 Planarity : 0.003 0.050 2577 Dihedral : 5.554 57.580 2873 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.24 % Allowed : 16.23 % Favored : 81.53 % 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: -0.09 (0.21), residues: 1619 helix: 1.18 (0.28), residues: 369 sheet: 0.33 (0.25), residues: 389 loop : -0.78 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 631 HIS 0.006 0.001 HIS E 374 PHE 0.011 0.001 PHE A 376 TYR 0.021 0.001 TYR A 165 ARG 0.007 0.001 ARG E 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 33) link_NAG-ASN : angle 1.89499 ( 99) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 1.65919 ( 27) link_ALPHA1-3 : bond 0.00927 ( 1) link_ALPHA1-3 : angle 1.67667 ( 3) hydrogen bonds : bond 0.03795 ( 444) hydrogen bonds : angle 4.74249 ( 1167) SS BOND : bond 0.00266 ( 33) SS BOND : angle 1.38946 ( 66) covalent geometry : bond 0.00255 (15054) covalent geometry : angle 0.55307 (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 322 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8272 (tm-30) REVERT: A 153 MET cc_start: 0.8264 (ttm) cc_final: 0.7959 (ttm) REVERT: A 265 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8782 (mp) REVERT: A 267 GLU cc_start: 0.7882 (tp30) cc_final: 0.7651 (tp30) REVERT: A 500 ARG cc_start: 0.6131 (ttt-90) cc_final: 0.5829 (ttt-90) REVERT: C 540 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.6717 (mp10) REVERT: C 588 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6238 (tmm-80) REVERT: C 634 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8441 (mt-10) REVERT: E 114 GLN cc_start: 0.8494 (tt0) cc_final: 0.8194 (tt0) REVERT: E 157 LEU cc_start: 0.8048 (mt) cc_final: 0.7818 (mp) REVERT: E 233 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6039 (p90) REVERT: E 391 PHE cc_start: 0.8396 (m-80) cc_final: 0.8170 (m-80) REVERT: E 475 MET cc_start: 0.7929 (mmt) cc_final: 0.7618 (mmt) REVERT: D 543 ASN cc_start: 0.8314 (m-40) cc_final: 0.7986 (m110) REVERT: D 585 ARG cc_start: 0.9012 (mmm-85) cc_final: 0.8643 (mtm-85) REVERT: F 486 TYR cc_start: 0.8901 (m-80) cc_final: 0.8232 (m-10) REVERT: F 490 LYS cc_start: 0.8863 (tttm) cc_final: 0.8598 (tttp) outliers start: 33 outliers final: 25 residues processed: 312 average time/residue: 0.2575 time to fit residues: 117.1407 Evaluate side-chains 301 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 347 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 649 SER 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 208 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 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 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 450 THR 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: 1.9990 chunk 155 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 101 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.172909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143043 restraints weight = 19960.089| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.50 r_work: 0.3460 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15130 Z= 0.123 Angle : 0.580 9.339 20667 Z= 0.289 Chirality : 0.043 0.189 2490 Planarity : 0.003 0.051 2577 Dihedral : 5.433 57.660 2873 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.17 % Allowed : 16.50 % Favored : 81.33 % 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: -0.05 (0.21), residues: 1619 helix: 1.23 (0.28), residues: 370 sheet: 0.30 (0.25), residues: 405 loop : -0.76 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 631 HIS 0.005 0.001 HIS E 374 PHE 0.028 0.001 PHE A 53 TYR 0.021 0.001 TYR A 165 ARG 0.010 0.001 ARG C 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 33) link_NAG-ASN : angle 1.84406 ( 99) link_BETA1-4 : bond 0.00436 ( 9) link_BETA1-4 : angle 1.66644 ( 27) link_ALPHA1-3 : bond 0.00907 ( 1) link_ALPHA1-3 : angle 1.74370 ( 3) hydrogen bonds : bond 0.03805 ( 444) hydrogen bonds : angle 4.73071 ( 1167) SS BOND : bond 0.00337 ( 33) SS BOND : angle 1.52968 ( 66) covalent geometry : bond 0.00285 (15054) covalent geometry : angle 0.55783 (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: 32 poor density : 287 time to evaluate : 1.531 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 51 THR cc_start: 0.9636 (m) cc_final: 0.9433 (p) REVERT: A 142 MET cc_start: 0.8261 (mmm) cc_final: 0.7826 (mmt) REVERT: A 153 MET cc_start: 0.7960 (ttm) cc_final: 0.7657 (ttm) REVERT: A 265 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8736 (mp) REVERT: A 500 ARG cc_start: 0.6086 (ttt-90) cc_final: 0.5853 (ttt-90) REVERT: C 540 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.6638 (mp10) REVERT: C 588 ARG cc_start: 0.7094 (mtt180) cc_final: 0.6174 (tmm-80) REVERT: C 634 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8365 (mt-10) REVERT: E 114 GLN cc_start: 0.8326 (tt0) cc_final: 0.8025 (tt0) REVERT: E 156 GLU cc_start: 0.7725 (mp0) cc_final: 0.6796 (mt-10) REVERT: E 233 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6087 (p90) REVERT: E 391 PHE cc_start: 0.8357 (m-80) cc_final: 0.8129 (m-80) REVERT: E 475 MET cc_start: 0.7866 (mmt) cc_final: 0.7465 (mmt) REVERT: D 543 ASN cc_start: 0.8200 (m-40) cc_final: 0.7886 (m-40) REVERT: D 585 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8490 (mtm-85) REVERT: F 316 TRP cc_start: 0.8169 (m100) cc_final: 0.7853 (m100) REVERT: F 486 TYR cc_start: 0.8853 (m-80) cc_final: 0.8248 (m-10) REVERT: F 490 LYS cc_start: 0.8822 (tttm) cc_final: 0.8538 (tttp) outliers start: 32 outliers final: 27 residues processed: 308 average time/residue: 0.2667 time to fit residues: 120.0007 Evaluate side-chains 311 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 281 time to evaluate : 1.682 ------------------------------------------------------------------------------- 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 347 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 649 SER 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 196 CYS Chi-restraints excluded: chain E residue 208 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 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 240 THR 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 450 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 0.0060 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN E 348 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 = 0.3888 r_free = 0.3888 target = 0.170341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140358 restraints weight = 20179.794| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.48 r_work: 0.3408 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15130 Z= 0.171 Angle : 0.624 9.457 20667 Z= 0.310 Chirality : 0.044 0.195 2490 Planarity : 0.004 0.053 2577 Dihedral : 5.557 45.414 2873 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.97 % Allowed : 16.97 % Favored : 81.06 % 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: -0.14 (0.21), residues: 1619 helix: 1.14 (0.28), residues: 370 sheet: 0.23 (0.25), residues: 409 loop : -0.80 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 631 HIS 0.005 0.001 HIS E 374 PHE 0.026 0.002 PHE A 53 TYR 0.022 0.002 TYR A 165 ARG 0.011 0.001 ARG C 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 33) link_NAG-ASN : angle 1.92380 ( 99) link_BETA1-4 : bond 0.00407 ( 9) link_BETA1-4 : angle 1.82597 ( 27) link_ALPHA1-3 : bond 0.00780 ( 1) link_ALPHA1-3 : angle 1.80392 ( 3) hydrogen bonds : bond 0.04140 ( 444) hydrogen bonds : angle 4.83415 ( 1167) SS BOND : bond 0.00430 ( 33) SS BOND : angle 1.56344 ( 66) covalent geometry : bond 0.00406 (15054) covalent geometry : angle 0.60192 (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 310 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 281 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8511 (mmm) cc_final: 0.8005 (mmt) REVERT: A 153 MET cc_start: 0.8290 (ttm) cc_final: 0.7999 (ttm) REVERT: A 265 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 500 ARG cc_start: 0.6325 (ttt-90) cc_final: 0.6042 (ttt-90) REVERT: C 540 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: C 634 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8468 (mt-10) REVERT: E 114 GLN cc_start: 0.8484 (tt0) cc_final: 0.8181 (tt0) REVERT: E 156 GLU cc_start: 0.7826 (mp0) cc_final: 0.6927 (mt-10) REVERT: E 233 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6188 (p90) REVERT: D 543 ASN cc_start: 0.8246 (m-40) cc_final: 0.7890 (m110) REVERT: D 579 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7462 (mtt180) REVERT: D 585 ARG cc_start: 0.9077 (mmm-85) cc_final: 0.8688 (mtm-85) REVERT: F 316 TRP cc_start: 0.8185 (m100) cc_final: 0.7837 (m100) REVERT: F 490 LYS cc_start: 0.8914 (tttm) cc_final: 0.8623 (tttp) outliers start: 29 outliers final: 26 residues processed: 301 average time/residue: 0.2750 time to fit residues: 121.1418 Evaluate side-chains 307 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 347 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 649 SER 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 196 CYS Chi-restraints excluded: chain E residue 208 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 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 Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 57 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.169147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139032 restraints weight = 20150.146| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.52 r_work: 0.3410 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15130 Z= 0.198 Angle : 0.668 10.927 20667 Z= 0.330 Chirality : 0.045 0.202 2490 Planarity : 0.004 0.053 2577 Dihedral : 5.775 45.731 2873 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.65 % Allowed : 16.50 % Favored : 80.86 % 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: -0.32 (0.21), residues: 1619 helix: 0.99 (0.28), residues: 367 sheet: -0.04 (0.25), residues: 421 loop : -0.82 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 338 HIS 0.005 0.001 HIS E 374 PHE 0.026 0.002 PHE A 53 TYR 0.022 0.002 TYR A 165 ARG 0.010 0.001 ARG C 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 33) link_NAG-ASN : angle 2.02420 ( 99) link_BETA1-4 : bond 0.00388 ( 9) link_BETA1-4 : angle 1.93289 ( 27) link_ALPHA1-3 : bond 0.00794 ( 1) link_ALPHA1-3 : angle 1.92210 ( 3) hydrogen bonds : bond 0.04445 ( 444) hydrogen bonds : angle 4.97784 ( 1167) SS BOND : bond 0.00441 ( 33) SS BOND : angle 1.60351 ( 66) covalent geometry : bond 0.00471 (15054) covalent geometry : angle 0.64572 (20472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7608.88 seconds wall clock time: 132 minutes 33.03 seconds (7953.03 seconds total)