Starting phenix.real_space_refine on Sun Nov 17 22:10:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/11_2024/8sww_40823.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/11_2024/8sww_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/11_2024/8sww_40823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/11_2024/8sww_40823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/11_2024/8sww_40823.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/11_2024/8sww_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14799 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3478 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "B" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "C" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 927 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3490 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 829 Classifications: {'peptide': 105} Link IDs: {'TRANS': 104} Chain breaks: 2 Chain: "F" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3427 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 3 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "L" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.74, per 1000 atoms: 0.66 Number of scatterers: 14799 At special positions: 0 Unit cell: (134.03, 139.185, 119.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2903 8.00 N 2565 7.00 C 9229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.06 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.12 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.08 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.05 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.02 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 149 " distance=2.01 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.02 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 152 " " NAG A 603 " - " ASN A 289 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 448 " " NAG A 606 " - " ASN A 363 " " NAG A 607 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 618 " " NAG C 702 " - " ASN C 637 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 448 " " NAG E 603 " - " ASN E 332 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 133 " " NAG E 606 " - " ASN E 88 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 152 " " NAG F 603 " - " ASN F 295 " " NAG F 604 " - " ASN F 301 " " NAG F 605 " - " ASN F 339 " " NAG F 606 " - " ASN F 392 " " NAG F 607 " - " ASN F 241 " " NAG F 608 " - " ASN F 276 " " NAG F 609 " - " ASN F 234 " " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN A 386 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN F 262 " " NAG O 1 " - " ASN F 332 " Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.5 seconds 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3546 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 27 sheets defined 26.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 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: 5.23 Time building geometry restraints manager: 4.61 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: 5.810 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.620 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.230 ------------------------------------------------------------------------------- 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 15054 Z= 1.334 Angle : 1.685 11.834 20472 Z= 1.096 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 *********************** 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 : 1.550 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: 0.2955 time to fit residues: 200.2322 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 : 1.608 ------------------------------------------------------------------------------- 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: 0.9980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 15054 Z= 0.236 Angle : 0.685 8.393 20472 Z= 0.352 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 *********************** 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 : 1.612 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: 0.8637 (t) cc_final: 0.8339 (p) REVERT: A 153 MET cc_start: 0.7466 (ttm) cc_final: 0.7263 (ttm) REVERT: A 434 MET cc_start: 0.8912 (ttp) cc_final: 0.8705 (ttm) REVERT: B 540 GLN cc_start: 0.4447 (mm-40) cc_final: 0.4020 (mm-40) REVERT: C 621 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7184 (mt-10) REVERT: E 114 GLN cc_start: 0.8228 (tt0) cc_final: 0.7973 (tt0) REVERT: E 153 MET cc_start: 0.8248 (tpp) cc_final: 0.7381 (tpp) REVERT: E 238 PRO cc_start: 0.8194 (Cg_endo) cc_final: 0.7720 (Cg_exo) REVERT: E 500 ARG cc_start: 0.6460 (mmt180) cc_final: 0.6002 (mtt180) REVERT: F 153 MET cc_start: 0.7408 (ptp) cc_final: 0.6873 (ptt) outliers start: 28 outliers final: 20 residues processed: 365 average time/residue: 0.2959 time to fit residues: 157.2730 Evaluate side-chains 292 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.0010 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 162 GLN E 195 ASN E 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15054 Z= 0.298 Angle : 0.652 8.544 20472 Z= 0.335 Chirality : 0.046 0.196 2490 Planarity : 0.004 0.045 2577 Dihedral : 5.998 45.783 2873 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.99 % Allowed : 11.74 % Favored : 85.27 % 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: 0.27 (0.20), residues: 1619 helix: 1.12 (0.28), residues: 369 sheet: 0.67 (0.24), residues: 403 loop : -0.45 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 479 HIS 0.008 0.002 HIS E 352 PHE 0.020 0.002 PHE A 376 TYR 0.021 0.002 TYR A 191 ARG 0.006 0.001 ARG E 504 *********************** 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 338 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 1.643 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: 0.8549 (t) cc_final: 0.8224 (p) REVERT: A 142 MET cc_start: 0.8013 (mtp) cc_final: 0.7745 (mtp) REVERT: A 153 MET cc_start: 0.7542 (ttm) cc_final: 0.7299 (ttm) REVERT: A 267 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7227 (mm-30) REVERT: A 434 MET cc_start: 0.8953 (ttp) cc_final: 0.8724 (ttm) REVERT: E 233 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.6281 (p90) REVERT: E 500 ARG cc_start: 0.6692 (mmt180) cc_final: 0.6105 (mtt180) REVERT: D 585 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8202 (mmm-85) REVERT: F 153 MET cc_start: 0.7414 (ptp) cc_final: 0.6706 (ptt) outliers start: 44 outliers final: 30 residues processed: 322 average time/residue: 0.2820 time to fit residues: 132.0873 Evaluate side-chains 292 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 A residue 244 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain C residue 630 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 154 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 326 ILE 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 166 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 374 HIS A 422 GLN B 540 GLN E 99 ASN E 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 15054 Z= 0.465 Angle : 0.781 10.149 20472 Z= 0.395 Chirality : 0.050 0.227 2490 Planarity : 0.005 0.055 2577 Dihedral : 6.770 54.019 2873 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.48 % Allowed : 11.07 % Favored : 84.45 % 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: -0.48 (0.20), residues: 1619 helix: 0.59 (0.27), residues: 375 sheet: 0.02 (0.25), residues: 394 loop : -0.87 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 479 HIS 0.008 0.002 HIS A 105 PHE 0.027 0.003 PHE A 376 TYR 0.022 0.002 TYR A 191 ARG 0.011 0.001 ARG C 617 *********************** 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 350 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 284 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8571 (t) cc_final: 0.8255 (p) REVERT: A 153 MET cc_start: 0.7545 (ttm) cc_final: 0.7231 (ttm) REVERT: A 342 LEU cc_start: 0.9066 (tp) cc_final: 0.8836 (tp) REVERT: A 434 MET cc_start: 0.9016 (ttp) cc_final: 0.8763 (ttm) REVERT: C 540 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.6872 (mp10) REVERT: C 634 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7909 (mt-10) REVERT: E 156 GLU cc_start: 0.7677 (mp0) cc_final: 0.7088 (mt-10) REVERT: E 233 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6760 (p90) REVERT: D 543 ASN cc_start: 0.8258 (m-40) cc_final: 0.7986 (m110) REVERT: D 579 ARG cc_start: 0.7884 (mtp180) cc_final: 0.7333 (mtp85) REVERT: F 153 MET cc_start: 0.7400 (ptp) cc_final: 0.6967 (ptt) outliers start: 66 outliers final: 48 residues processed: 329 average time/residue: 0.2855 time to fit residues: 136.5391 Evaluate side-chains 314 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain A residue 138 ILE 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 346 VAL Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 52 LEU 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 236 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 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 450 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 0.0270 chunk 123 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15054 Z= 0.185 Angle : 0.581 7.663 20472 Z= 0.297 Chirality : 0.043 0.200 2490 Planarity : 0.003 0.049 2577 Dihedral : 5.968 55.745 2873 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.51 % Allowed : 14.26 % Favored : 83.23 % 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: -0.22 (0.20), residues: 1619 helix: 0.92 (0.28), residues: 375 sheet: 0.10 (0.24), residues: 416 loop : -0.73 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 623 HIS 0.008 0.001 HIS E 374 PHE 0.014 0.001 PHE A 376 TYR 0.024 0.002 TYR A 165 ARG 0.011 0.001 ARG C 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 293 time to evaluate : 1.593 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: 0.8590 (t) cc_final: 0.8300 (p) REVERT: A 153 MET cc_start: 0.7359 (ttm) cc_final: 0.7079 (ttm) REVERT: A 342 LEU cc_start: 0.8917 (tp) cc_final: 0.8694 (tp) REVERT: A 434 MET cc_start: 0.8958 (ttp) cc_final: 0.8707 (ttm) REVERT: A 500 ARG cc_start: 0.6612 (ttt-90) cc_final: 0.6197 (ttt-90) REVERT: B 626 MET cc_start: 0.7810 (ttm) cc_final: 0.7576 (ttm) REVERT: C 540 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.6861 (mp10) REVERT: C 634 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7828 (mt-10) REVERT: E 114 GLN cc_start: 0.8268 (tt0) cc_final: 0.8026 (tt0) REVERT: E 156 GLU cc_start: 0.7559 (mp0) cc_final: 0.7100 (mt-10) REVERT: E 233 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.5811 (p90) REVERT: F 486 TYR cc_start: 0.8724 (m-80) cc_final: 0.8321 (m-10) outliers start: 37 outliers final: 26 residues processed: 320 average time/residue: 0.3121 time to fit residues: 147.9738 Evaluate side-chains 302 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 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 E residue 233 PHE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 294 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 501 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.0980 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 0.0270 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15054 Z= 0.186 Angle : 0.560 8.038 20472 Z= 0.284 Chirality : 0.043 0.198 2490 Planarity : 0.003 0.048 2577 Dihedral : 5.639 58.682 2873 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.05 % Allowed : 14.60 % Favored : 82.35 % 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: -0.09 (0.21), residues: 1619 helix: 1.09 (0.28), residues: 375 sheet: 0.26 (0.25), residues: 411 loop : -0.74 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 631 HIS 0.008 0.001 HIS E 374 PHE 0.015 0.001 PHE A 376 TYR 0.020 0.002 TYR A 165 ARG 0.010 0.001 ARG B 617 *********************** 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 334 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 289 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8571 (t) cc_final: 0.8309 (p) REVERT: A 142 MET cc_start: 0.7867 (mtp) cc_final: 0.7471 (mtp) REVERT: A 153 MET cc_start: 0.7354 (ttm) cc_final: 0.7087 (ttm) REVERT: A 434 MET cc_start: 0.8946 (ttp) cc_final: 0.8660 (ttm) REVERT: A 500 ARG cc_start: 0.6431 (ttt-90) cc_final: 0.6216 (ttt-90) REVERT: C 540 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: C 634 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7820 (mt-10) REVERT: E 157 LEU cc_start: 0.8689 (mt) cc_final: 0.8427 (mp) REVERT: E 233 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.5773 (p90) REVERT: E 475 MET cc_start: 0.7695 (mmt) cc_final: 0.7354 (mmt) REVERT: F 486 TYR cc_start: 0.8654 (m-80) cc_final: 0.8317 (m-10) outliers start: 45 outliers final: 32 residues processed: 319 average time/residue: 0.2734 time to fit residues: 128.0643 Evaluate side-chains 309 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 340 GLU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 488 VAL 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 52 LEU 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 255 VAL Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain D residue 534 SER 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 157 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 439 ILE 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 172 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN E 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15054 Z= 0.280 Angle : 0.614 13.507 20472 Z= 0.309 Chirality : 0.045 0.201 2490 Planarity : 0.003 0.049 2577 Dihedral : 5.830 57.111 2873 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.33 % Allowed : 14.94 % Favored : 81.74 % 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: -0.22 (0.21), residues: 1619 helix: 0.95 (0.28), residues: 376 sheet: 0.18 (0.25), residues: 399 loop : -0.79 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 631 HIS 0.007 0.001 HIS E 374 PHE 0.019 0.002 PHE A 376 TYR 0.021 0.002 TYR A 165 ARG 0.007 0.001 ARG E 143 *********************** 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 333 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 284 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8591 (t) cc_final: 0.8336 (p) REVERT: A 153 MET cc_start: 0.7416 (ttm) cc_final: 0.7140 (ttm) REVERT: A 434 MET cc_start: 0.8968 (ttp) cc_final: 0.8710 (ttm) REVERT: A 500 ARG cc_start: 0.6554 (ttt-90) cc_final: 0.6346 (ttt-90) REVERT: C 540 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: C 634 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7772 (mt-10) REVERT: E 233 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.5890 (p90) REVERT: D 543 ASN cc_start: 0.7998 (m-40) cc_final: 0.7785 (m110) REVERT: D 579 ARG cc_start: 0.7805 (mtp180) cc_final: 0.7225 (mtp85) REVERT: F 486 TYR cc_start: 0.8765 (m-80) cc_final: 0.8437 (m-10) outliers start: 49 outliers final: 39 residues processed: 316 average time/residue: 0.2900 time to fit residues: 133.0682 Evaluate side-chains 318 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 277 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain 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 52 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 87 GLU 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 293 GLN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 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 450 THR 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 71 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 0.0170 chunk 162 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15054 Z= 0.170 Angle : 0.550 8.716 20472 Z= 0.281 Chirality : 0.043 0.193 2490 Planarity : 0.003 0.053 2577 Dihedral : 5.540 53.464 2873 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.51 % Allowed : 15.75 % Favored : 81.74 % 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: -0.15 (0.21), residues: 1619 helix: 0.96 (0.28), residues: 383 sheet: 0.26 (0.25), residues: 401 loop : -0.75 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 631 HIS 0.005 0.001 HIS E 374 PHE 0.013 0.001 PHE A 376 TYR 0.021 0.001 TYR A 165 ARG 0.015 0.001 ARG C 617 *********************** 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 321 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8586 (t) cc_final: 0.8366 (p) REVERT: A 153 MET cc_start: 0.7346 (ttm) cc_final: 0.7071 (ttm) REVERT: A 434 MET cc_start: 0.8940 (ttp) cc_final: 0.8662 (ttm) REVERT: B 617 ARG cc_start: 0.7420 (mtp-110) cc_final: 0.7099 (mtp85) REVERT: C 540 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: C 634 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7755 (mt-10) REVERT: E 114 GLN cc_start: 0.8246 (tt0) cc_final: 0.8006 (tt0) REVERT: E 156 GLU cc_start: 0.7639 (mp0) cc_final: 0.7009 (mt-10) REVERT: E 233 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.5759 (p90) REVERT: E 475 MET cc_start: 0.7703 (mmt) cc_final: 0.7318 (mmt) REVERT: F 87 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8159 (pp20) REVERT: F 486 TYR cc_start: 0.8634 (m-80) cc_final: 0.8139 (m-10) outliers start: 37 outliers final: 28 residues processed: 312 average time/residue: 0.2968 time to fit residues: 133.4837 Evaluate side-chains 304 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 340 GLU 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 52 LEU Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 439 ILE 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 170 optimal weight: 6.9990 chunk 155 optimal weight: 0.5980 chunk 166 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 0.0000 chunk 165 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15054 Z= 0.237 Angle : 0.585 8.792 20472 Z= 0.296 Chirality : 0.044 0.195 2490 Planarity : 0.004 0.053 2577 Dihedral : 5.598 58.033 2873 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.78 % Allowed : 15.61 % Favored : 81.60 % 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: -0.18 (0.21), residues: 1619 helix: 1.00 (0.28), residues: 377 sheet: 0.21 (0.25), residues: 399 loop : -0.78 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 338 HIS 0.006 0.001 HIS E 374 PHE 0.026 0.002 PHE A 53 TYR 0.020 0.002 TYR A 165 ARG 0.010 0.001 ARG A 143 *********************** 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 315 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8624 (t) cc_final: 0.8380 (p) REVERT: A 153 MET cc_start: 0.7328 (ttm) cc_final: 0.7069 (ttm) REVERT: A 434 MET cc_start: 0.8960 (ttp) cc_final: 0.8681 (ttm) REVERT: C 540 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.6866 (mp10) REVERT: E 114 GLN cc_start: 0.8274 (tt0) cc_final: 0.8029 (tt0) REVERT: E 156 GLU cc_start: 0.7653 (mp0) cc_final: 0.7056 (mt-10) REVERT: E 233 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6024 (p90) REVERT: E 475 MET cc_start: 0.7801 (mmt) cc_final: 0.7394 (mmt) REVERT: D 579 ARG cc_start: 0.7789 (mtp180) cc_final: 0.7509 (mtt180) REVERT: F 486 TYR cc_start: 0.8670 (m-80) cc_final: 0.8321 (m-10) outliers start: 41 outliers final: 35 residues processed: 302 average time/residue: 0.2945 time to fit residues: 129.1412 Evaluate side-chains 307 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 302 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain 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 255 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 87 GLU 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 293 GLN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN E 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15054 Z= 0.352 Angle : 0.652 9.252 20472 Z= 0.329 Chirality : 0.046 0.200 2490 Planarity : 0.004 0.056 2577 Dihedral : 5.861 55.544 2873 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.85 % Allowed : 15.82 % 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: -0.33 (0.21), residues: 1619 helix: 0.83 (0.28), residues: 379 sheet: 0.09 (0.26), residues: 393 loop : -0.83 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 338 HIS 0.006 0.002 HIS E 374 PHE 0.026 0.002 PHE A 53 TYR 0.021 0.002 TYR A 165 ARG 0.011 0.001 ARG C 617 ********************** 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 322 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8627 (t) cc_final: 0.8411 (p) REVERT: A 153 MET cc_start: 0.7380 (ttm) cc_final: 0.7109 (ttm) REVERT: A 434 MET cc_start: 0.8976 (ttp) cc_final: 0.8681 (ttm) REVERT: C 540 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.6837 (mp10) REVERT: E 156 GLU cc_start: 0.7728 (mp0) cc_final: 0.7086 (mt-10) REVERT: E 233 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.5973 (p90) REVERT: D 579 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7285 (mtp85) REVERT: F 486 TYR cc_start: 0.8756 (m-80) cc_final: 0.8530 (m-10) outliers start: 42 outliers final: 36 residues processed: 306 average time/residue: 0.3003 time to fit residues: 134.0319 Evaluate side-chains 319 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 302 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain 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 100 MET Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 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 255 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain D residue 534 SER 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 87 GLU 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 293 GLN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 439 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN E 99 ASN E 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.172782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.144358 restraints weight = 19993.586| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.30 r_work: 0.3464 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15054 Z= 0.176 Angle : 0.572 9.092 20472 Z= 0.293 Chirality : 0.043 0.189 2490 Planarity : 0.004 0.057 2577 Dihedral : 5.478 48.025 2873 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.85 % Allowed : 16.36 % Favored : 80.79 % 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: -0.22 (0.21), residues: 1619 helix: 1.02 (0.28), residues: 376 sheet: 0.15 (0.26), residues: 399 loop : -0.81 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 338 HIS 0.005 0.001 HIS E 374 PHE 0.025 0.001 PHE A 53 TYR 0.022 0.001 TYR A 165 ARG 0.009 0.001 ARG C 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3701.74 seconds wall clock time: 69 minutes 42.67 seconds (4182.67 seconds total)