Starting phenix.real_space_refine on Sat Aug 23 21:13:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sww_40823/08_2025/8sww_40823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sww_40823/08_2025/8sww_40823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sww_40823/08_2025/8sww_40823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sww_40823/08_2025/8sww_40823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sww_40823/08_2025/8sww_40823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sww_40823/08_2025/8sww_40823.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.04, per 1000 atoms: 0.27 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: 1.34 Conformation dependent library (CDL) restraints added in 699.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.59 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: 2.52 Time building geometry restraints manager: 1.78 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.500 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.154 15130 Z= 1.117 Angle : 1.710 11.834 20667 Z= 1.098 Chirality : 0.124 0.510 2490 Planarity : 0.009 0.050 2577 Dihedral : 10.733 109.419 5996 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG C 542 TYR 0.041 0.007 TYR F 191 PHE 0.032 0.007 PHE E 376 TRP 0.050 0.010 TRP A 69 HIS 0.015 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.02101 (15054) covalent geometry : angle 1.68533 (20472) SS BOND : bond 0.02083 ( 33) SS BOND : angle 3.21469 ( 66) hydrogen bonds : bond 0.15691 ( 444) hydrogen bonds : angle 6.98809 ( 1167) link_ALPHA1-3 : bond 0.08547 ( 1) link_ALPHA1-3 : angle 4.78192 ( 3) link_BETA1-4 : bond 0.07143 ( 9) link_BETA1-4 : angle 5.17536 ( 27) link_NAG-ASN : bond 0.07899 ( 33) link_NAG-ASN : angle 2.80298 ( 99) *********************** 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 : 0.704 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: 0.8260 (ttmm) REVERT: A 434 MET cc_start: 0.9062 (ttp) cc_final: 0.8810 (ttm) REVERT: E 128 THR cc_start: 0.9024 (m) cc_final: 0.8816 (p) REVERT: E 274 SER cc_start: 0.8326 (t) cc_final: 0.8123 (p) REVERT: E 351 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7485 (ttmm) REVERT: E 500 ARG cc_start: 0.6413 (mmt180) cc_final: 0.5707 (mtt180) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.1405 time to fit residues: 96.1054 Evaluate side-chains 282 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 287 GLN A 425 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN C 630 GLN E 328 GLN E 352 HIS F 300 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.177469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.147278 restraints weight = 19956.146| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.54 r_work: 0.3506 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15130 Z= 0.196 Angle : 0.749 8.390 20667 Z= 0.374 Chirality : 0.047 0.219 2490 Planarity : 0.004 0.037 2577 Dihedral : 7.033 65.189 2873 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.10 % Allowed : 9.78 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.20), residues: 1619 helix: 1.10 (0.28), residues: 364 sheet: 1.01 (0.24), residues: 405 loop : -0.22 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 476 TYR 0.023 0.002 TYR B 638 PHE 0.020 0.002 PHE F 353 TRP 0.025 0.002 TRP E 479 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00450 (15054) covalent geometry : angle 0.70624 (20472) SS BOND : bond 0.00415 ( 33) SS BOND : angle 1.15111 ( 66) hydrogen bonds : bond 0.05701 ( 444) hydrogen bonds : angle 5.51767 ( 1167) link_ALPHA1-3 : bond 0.02106 ( 1) link_ALPHA1-3 : angle 1.11418 ( 3) link_BETA1-4 : bond 0.00608 ( 9) link_BETA1-4 : angle 3.16681 ( 27) link_NAG-ASN : bond 0.00532 ( 33) link_NAG-ASN : angle 3.20091 ( 99) *********************** 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 366 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 335 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8590 (t) cc_final: 0.8224 (p) REVERT: A 153 MET cc_start: 0.8142 (ttm) cc_final: 0.7872 (ttm) REVERT: A 434 MET cc_start: 0.9112 (ttp) cc_final: 0.8891 (ttm) REVERT: B 540 GLN cc_start: 0.5079 (mm-40) cc_final: 0.4734 (mm-40) REVERT: C 621 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7202 (mt-10) REVERT: C 651 ASN cc_start: 0.8843 (t0) cc_final: 0.8632 (t0) REVERT: E 114 GLN cc_start: 0.8425 (tt0) cc_final: 0.8069 (tt0) REVERT: E 140 ASP cc_start: 0.6672 (m-30) cc_final: 0.6320 (t0) REVERT: E 233 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.4819 (p90) REVERT: E 238 PRO cc_start: 0.8311 (Cg_endo) cc_final: 0.7725 (Cg_exo) REVERT: E 500 ARG cc_start: 0.6492 (mmt180) cc_final: 0.5860 (mtt180) REVERT: F 153 MET cc_start: 0.7564 (ptp) cc_final: 0.6809 (ptt) REVERT: F 490 LYS cc_start: 0.8664 (tttp) cc_final: 0.8217 (tttp) outliers start: 31 outliers final: 23 residues processed: 355 average time/residue: 0.1323 time to fit residues: 68.4535 Evaluate side-chains 292 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 323 ILE 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 E residue 233 PHE Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 90 THR 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 393 SER Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 103 GLN E 162 GLN E 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.172514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142249 restraints weight = 20103.117| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.52 r_work: 0.3447 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 15130 Z= 0.208 Angle : 0.699 9.128 20667 Z= 0.348 Chirality : 0.047 0.193 2490 Planarity : 0.004 0.037 2577 Dihedral : 6.137 45.490 2873 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.26 % Allowed : 10.93 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.20), residues: 1619 helix: 1.10 (0.28), residues: 366 sheet: 0.65 (0.24), residues: 403 loop : -0.50 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 504 TYR 0.016 0.002 TYR E 486 PHE 0.020 0.002 PHE A 376 TRP 0.018 0.002 TRP C 623 HIS 0.008 0.002 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00484 (15054) covalent geometry : angle 0.66849 (20472) SS BOND : bond 0.00452 ( 33) SS BOND : angle 1.28751 ( 66) hydrogen bonds : bond 0.05056 ( 444) hydrogen bonds : angle 5.20016 ( 1167) link_ALPHA1-3 : bond 0.01191 ( 1) link_ALPHA1-3 : angle 1.98623 ( 3) link_BETA1-4 : bond 0.00593 ( 9) link_BETA1-4 : angle 2.52817 ( 27) link_NAG-ASN : bond 0.00425 ( 33) link_NAG-ASN : angle 2.55789 ( 99) *********************** 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: 48 poor density : 290 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8587 (t) cc_final: 0.8193 (p) REVERT: A 153 MET cc_start: 0.8181 (ttm) cc_final: 0.7839 (ttm) REVERT: A 190 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7881 (mp0) REVERT: A 268 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6961 (mm-30) REVERT: A 280 ASN cc_start: 0.8290 (m-40) cc_final: 0.8082 (m110) REVERT: A 434 MET cc_start: 0.9208 (ttp) cc_final: 0.8994 (ttm) REVERT: C 617 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7277 (mtp85) REVERT: C 621 GLU cc_start: 0.7682 (mt-10) cc_final: 0.6982 (mt-10) REVERT: E 140 ASP cc_start: 0.6919 (m-30) cc_final: 0.6515 (t0) REVERT: E 156 GLU cc_start: 0.7791 (mp0) cc_final: 0.7189 (mt-10) REVERT: E 233 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6284 (p90) REVERT: E 500 ARG cc_start: 0.6827 (mmt180) cc_final: 0.6037 (mtt180) REVERT: F 490 LYS cc_start: 0.8755 (tttp) cc_final: 0.8508 (tttp) outliers start: 48 outliers final: 32 residues processed: 322 average time/residue: 0.1299 time to fit residues: 61.0966 Evaluate side-chains 294 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 163 LYS 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 346 VAL Chi-restraints excluded: chain A residue 371 VAL 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 254 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 99 ASN 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 118 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 152 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN E 103 GLN E 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.174579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.145452 restraints weight = 20051.453| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.44 r_work: 0.3450 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15130 Z= 0.176 Angle : 0.637 9.527 20667 Z= 0.317 Chirality : 0.045 0.195 2490 Planarity : 0.004 0.045 2577 Dihedral : 5.801 44.212 2873 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.26 % Allowed : 12.08 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1619 helix: 1.04 (0.28), residues: 372 sheet: 0.42 (0.23), residues: 430 loop : -0.67 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 469 TYR 0.015 0.002 TYR E 486 PHE 0.019 0.002 PHE A 376 TRP 0.018 0.002 TRP E 479 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00408 (15054) covalent geometry : angle 0.61146 (20472) SS BOND : bond 0.00452 ( 33) SS BOND : angle 0.88903 ( 66) hydrogen bonds : bond 0.04483 ( 444) hydrogen bonds : angle 5.00679 ( 1167) link_ALPHA1-3 : bond 0.01064 ( 1) link_ALPHA1-3 : angle 2.29455 ( 3) link_BETA1-4 : bond 0.00526 ( 9) link_BETA1-4 : angle 2.18651 ( 27) link_NAG-ASN : bond 0.00366 ( 33) link_NAG-ASN : angle 2.34746 ( 99) *********************** 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 332 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8618 (t) cc_final: 0.8229 (p) REVERT: A 153 MET cc_start: 0.8362 (ttm) cc_final: 0.8057 (ttm) REVERT: A 265 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 434 MET cc_start: 0.9292 (ttp) cc_final: 0.9081 (ttm) REVERT: C 540 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.6663 (mp10) REVERT: C 634 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8428 (mt-10) REVERT: E 140 ASP cc_start: 0.6960 (m-30) cc_final: 0.6536 (t0) REVERT: E 156 GLU cc_start: 0.7768 (mp0) cc_final: 0.7251 (mt-10) REVERT: E 233 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.6460 (p90) REVERT: F 484 TYR cc_start: 0.8405 (p90) cc_final: 0.8176 (p90) REVERT: F 490 LYS cc_start: 0.8839 (tttp) cc_final: 0.8542 (tttp) outliers start: 48 outliers final: 30 residues processed: 317 average time/residue: 0.1335 time to fit residues: 61.8468 Evaluate side-chains 297 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 164 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 376 PHE 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 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 280 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 393 SER 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 119 optimal weight: 6.9990 chunk 69 optimal weight: 0.0170 chunk 173 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.143396 restraints weight = 20149.285| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.29 r_work: 0.3472 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15130 Z= 0.127 Angle : 0.589 9.141 20667 Z= 0.292 Chirality : 0.043 0.194 2490 Planarity : 0.003 0.043 2577 Dihedral : 5.506 43.388 2873 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.51 % Allowed : 13.78 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.20), residues: 1619 helix: 1.26 (0.28), residues: 363 sheet: 0.40 (0.24), residues: 430 loop : -0.67 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 617 TYR 0.025 0.002 TYR A 165 PHE 0.015 0.002 PHE A 53 TRP 0.015 0.001 TRP B 631 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00290 (15054) covalent geometry : angle 0.56520 (20472) SS BOND : bond 0.00331 ( 33) SS BOND : angle 0.99044 ( 66) hydrogen bonds : bond 0.04092 ( 444) hydrogen bonds : angle 4.86542 ( 1167) link_ALPHA1-3 : bond 0.01066 ( 1) link_ALPHA1-3 : angle 2.13657 ( 3) link_BETA1-4 : bond 0.00482 ( 9) link_BETA1-4 : angle 1.93707 ( 27) link_NAG-ASN : bond 0.00303 ( 33) link_NAG-ASN : angle 2.12747 ( 99) *********************** 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 315 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8618 (t) cc_final: 0.8285 (p) REVERT: A 142 MET cc_start: 0.8275 (mmm) cc_final: 0.7772 (mmt) REVERT: A 153 MET cc_start: 0.8239 (ttm) cc_final: 0.7903 (ttm) REVERT: A 190 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7981 (mp0) REVERT: A 434 MET cc_start: 0.9209 (ttp) cc_final: 0.8965 (ttm) REVERT: C 540 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.6745 (mp10) REVERT: C 634 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8427 (mt-10) REVERT: E 114 GLN cc_start: 0.8518 (tt0) cc_final: 0.8199 (tt0) REVERT: E 140 ASP cc_start: 0.6951 (m-30) cc_final: 0.6550 (t0) REVERT: E 156 GLU cc_start: 0.7672 (mp0) cc_final: 0.7236 (mt-10) REVERT: E 233 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.5362 (p90) REVERT: F 46 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8742 (mttm) REVERT: F 484 TYR cc_start: 0.8362 (p90) cc_final: 0.8141 (p90) REVERT: F 486 TYR cc_start: 0.8956 (m-80) cc_final: 0.8557 (m-10) REVERT: F 490 LYS cc_start: 0.8784 (tttp) cc_final: 0.8495 (tttp) outliers start: 37 outliers final: 31 residues processed: 302 average time/residue: 0.1332 time to fit residues: 58.8282 Evaluate side-chains 298 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 488 VAL 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 135 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 165 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 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 450 THR 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 161 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.138613 restraints weight = 20291.659| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.21 r_work: 0.3359 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15130 Z= 0.269 Angle : 0.733 9.203 20667 Z= 0.360 Chirality : 0.048 0.211 2490 Planarity : 0.004 0.046 2577 Dihedral : 6.288 56.396 2873 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.28 % Allowed : 13.24 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.20), residues: 1619 helix: 0.79 (0.28), residues: 372 sheet: -0.00 (0.25), residues: 400 loop : -0.81 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 617 TYR 0.018 0.002 TYR A 165 PHE 0.022 0.002 PHE A 376 TRP 0.019 0.002 TRP F 316 HIS 0.007 0.002 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00641 (15054) covalent geometry : angle 0.71028 (20472) SS BOND : bond 0.00514 ( 33) SS BOND : angle 1.14047 ( 66) hydrogen bonds : bond 0.05029 ( 444) hydrogen bonds : angle 5.15802 ( 1167) link_ALPHA1-3 : bond 0.00630 ( 1) link_ALPHA1-3 : angle 2.31703 ( 3) link_BETA1-4 : bond 0.00349 ( 9) link_BETA1-4 : angle 2.31626 ( 27) link_NAG-ASN : bond 0.00411 ( 33) link_NAG-ASN : angle 2.30820 ( 99) *********************** 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 340 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8667 (t) cc_final: 0.8334 (p) REVERT: A 142 MET cc_start: 0.8571 (mmm) cc_final: 0.8061 (mmt) REVERT: A 153 MET cc_start: 0.8365 (ttm) cc_final: 0.8058 (ttm) REVERT: A 265 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8805 (mp) REVERT: A 434 MET cc_start: 0.9228 (ttp) cc_final: 0.8994 (ttm) REVERT: C 540 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.6663 (mp10) REVERT: C 634 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8445 (mt-10) REVERT: E 140 ASP cc_start: 0.7075 (m-30) cc_final: 0.6564 (t0) REVERT: E 233 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6706 (p90) REVERT: E 475 MET cc_start: 0.7488 (mmp) cc_final: 0.7247 (mmt) REVERT: D 543 ASN cc_start: 0.8438 (m-40) cc_final: 0.8052 (m110) REVERT: D 579 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7253 (mtp85) REVERT: F 160 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7682 (mmmt) REVERT: F 484 TYR cc_start: 0.8456 (p90) cc_final: 0.8253 (p90) REVERT: F 490 LYS cc_start: 0.8889 (tttp) cc_final: 0.8581 (tttp) outliers start: 63 outliers final: 41 residues processed: 318 average time/residue: 0.1374 time to fit residues: 63.3360 Evaluate side-chains 316 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 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 145 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 326 ILE 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 636 SER Chi-restraints excluded: chain F residue 131 CYS 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 393 SER Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 180 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN E 103 GLN E 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.169728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141316 restraints weight = 20185.716| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.27 r_work: 0.3422 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15130 Z= 0.127 Angle : 0.602 10.011 20667 Z= 0.300 Chirality : 0.043 0.225 2490 Planarity : 0.003 0.043 2577 Dihedral : 5.890 59.172 2873 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.85 % Allowed : 14.73 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.20), residues: 1619 helix: 0.96 (0.28), residues: 372 sheet: 0.14 (0.25), residues: 401 loop : -0.77 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 617 TYR 0.015 0.001 TYR A 165 PHE 0.015 0.001 PHE A 376 TRP 0.019 0.001 TRP B 631 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00289 (15054) covalent geometry : angle 0.57865 (20472) SS BOND : bond 0.00353 ( 33) SS BOND : angle 1.18610 ( 66) hydrogen bonds : bond 0.04190 ( 444) hydrogen bonds : angle 4.87608 ( 1167) link_ALPHA1-3 : bond 0.00941 ( 1) link_ALPHA1-3 : angle 2.02795 ( 3) link_BETA1-4 : bond 0.00421 ( 9) link_BETA1-4 : angle 1.89465 ( 27) link_NAG-ASN : bond 0.00292 ( 33) link_NAG-ASN : angle 2.10685 ( 99) *********************** 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 327 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8641 (t) cc_final: 0.8342 (p) REVERT: A 142 MET cc_start: 0.8532 (mmm) cc_final: 0.8028 (mmt) REVERT: A 153 MET cc_start: 0.8255 (ttm) cc_final: 0.7964 (ttm) REVERT: A 265 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8809 (mp) REVERT: A 434 MET cc_start: 0.9214 (ttp) cc_final: 0.8965 (ttm) REVERT: A 500 ARG cc_start: 0.6224 (ttt-90) cc_final: 0.5688 (ttt-90) REVERT: C 540 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.6637 (mp10) REVERT: C 634 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8328 (mt-10) REVERT: E 114 GLN cc_start: 0.8430 (tt0) cc_final: 0.8090 (tt0) REVERT: E 140 ASP cc_start: 0.7018 (m-30) cc_final: 0.6562 (t0) REVERT: E 233 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.5731 (p90) REVERT: D 543 ASN cc_start: 0.8297 (m-40) cc_final: 0.7979 (m110) REVERT: D 579 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7232 (mtt180) REVERT: F 160 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7588 (tptp) REVERT: F 484 TYR cc_start: 0.8415 (p90) cc_final: 0.8192 (p90) REVERT: F 490 LYS cc_start: 0.8820 (tttp) cc_final: 0.8476 (tttp) outliers start: 42 outliers final: 29 residues processed: 314 average time/residue: 0.1346 time to fit residues: 61.3514 Evaluate side-chains 304 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 376 PHE 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 145 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 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 501 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 0.0970 chunk 182 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN F 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.168465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139981 restraints weight = 20280.185| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.26 r_work: 0.3406 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15130 Z= 0.174 Angle : 0.627 8.611 20667 Z= 0.310 Chirality : 0.045 0.200 2490 Planarity : 0.003 0.041 2577 Dihedral : 5.884 56.335 2873 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.85 % Allowed : 15.48 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.21), residues: 1619 helix: 0.97 (0.28), residues: 372 sheet: 0.06 (0.25), residues: 399 loop : -0.82 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 143 TYR 0.015 0.002 TYR A 165 PHE 0.019 0.002 PHE A 376 TRP 0.020 0.001 TRP B 631 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00411 (15054) covalent geometry : angle 0.60551 (20472) SS BOND : bond 0.00436 ( 33) SS BOND : angle 1.16906 ( 66) hydrogen bonds : bond 0.04303 ( 444) hydrogen bonds : angle 4.89000 ( 1167) link_ALPHA1-3 : bond 0.01006 ( 1) link_ALPHA1-3 : angle 2.06167 ( 3) link_BETA1-4 : bond 0.00405 ( 9) link_BETA1-4 : angle 1.95411 ( 27) link_NAG-ASN : bond 0.00305 ( 33) link_NAG-ASN : angle 2.04632 ( 99) *********************** 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 324 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8652 (t) cc_final: 0.8367 (p) REVERT: A 142 MET cc_start: 0.8607 (mmm) cc_final: 0.8103 (mmt) REVERT: A 153 MET cc_start: 0.8278 (ttm) cc_final: 0.7957 (ttm) REVERT: A 265 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 434 MET cc_start: 0.9212 (ttp) cc_final: 0.8961 (ttm) REVERT: A 500 ARG cc_start: 0.6138 (ttt-90) cc_final: 0.5656 (ttt-90) REVERT: C 540 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.6681 (mp10) REVERT: C 634 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8372 (mt-10) REVERT: E 140 ASP cc_start: 0.7069 (m-30) cc_final: 0.6614 (t0) REVERT: E 233 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.5845 (p90) REVERT: D 535 MET cc_start: 0.8892 (mmm) cc_final: 0.8642 (mpp) REVERT: D 543 ASN cc_start: 0.8340 (m-40) cc_final: 0.7975 (m110) REVERT: D 579 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7191 (mtp85) REVERT: F 160 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7653 (tptp) REVERT: F 486 TYR cc_start: 0.8990 (m-80) cc_final: 0.8621 (m-10) REVERT: F 490 LYS cc_start: 0.8879 (tttp) cc_final: 0.8618 (tttp) outliers start: 42 outliers final: 36 residues processed: 308 average time/residue: 0.1371 time to fit residues: 61.1989 Evaluate side-chains 316 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 376 PHE 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 100 MET Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 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 496 VAL Chi-restraints excluded: chain F residue 501 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 46 optimal weight: 0.0020 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 21 optimal weight: 0.1980 chunk 146 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.172972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142878 restraints weight = 20082.783| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.55 r_work: 0.3463 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15130 Z= 0.099 Angle : 0.553 10.242 20667 Z= 0.276 Chirality : 0.042 0.181 2490 Planarity : 0.003 0.045 2577 Dihedral : 5.406 55.975 2873 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.04 % Allowed : 16.43 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.21), residues: 1619 helix: 1.26 (0.28), residues: 367 sheet: 0.26 (0.25), residues: 401 loop : -0.76 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 617 TYR 0.022 0.001 TYR A 165 PHE 0.008 0.001 PHE A 376 TRP 0.025 0.001 TRP B 631 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00215 (15054) covalent geometry : angle 0.53567 (20472) SS BOND : bond 0.00383 ( 33) SS BOND : angle 0.82957 ( 66) hydrogen bonds : bond 0.03654 ( 444) hydrogen bonds : angle 4.68285 ( 1167) link_ALPHA1-3 : bond 0.00948 ( 1) link_ALPHA1-3 : angle 1.63602 ( 3) link_BETA1-4 : bond 0.00450 ( 9) link_BETA1-4 : angle 1.58286 ( 27) link_NAG-ASN : bond 0.00280 ( 33) link_NAG-ASN : angle 1.82904 ( 99) *********************** 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 323 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9618 (m) cc_final: 0.9413 (p) REVERT: A 142 MET cc_start: 0.8476 (mmm) cc_final: 0.6870 (mmt) REVERT: A 153 MET cc_start: 0.7953 (ttm) cc_final: 0.7639 (ttm) REVERT: A 265 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 434 MET cc_start: 0.9116 (ttp) cc_final: 0.8831 (ttm) REVERT: A 500 ARG cc_start: 0.6126 (ttt-90) cc_final: 0.5717 (ttt-90) REVERT: C 540 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: C 588 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6163 (tmm-80) REVERT: C 634 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8313 (mt-10) REVERT: E 114 GLN cc_start: 0.8301 (tt0) cc_final: 0.8002 (tt0) REVERT: E 140 ASP cc_start: 0.6995 (m-30) cc_final: 0.6623 (t0) REVERT: E 233 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.5670 (p90) REVERT: E 432 GLN cc_start: 0.8321 (mp10) cc_final: 0.8085 (mp10) REVERT: F 160 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7583 (tptp) REVERT: F 316 TRP cc_start: 0.8124 (m100) cc_final: 0.7803 (m100) REVERT: F 486 TYR cc_start: 0.8815 (m-80) cc_final: 0.8226 (m-10) outliers start: 30 outliers final: 23 residues processed: 313 average time/residue: 0.1404 time to fit residues: 62.9214 Evaluate side-chains 299 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain 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 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 GLU 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 633 LYS 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 450 THR 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 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 137 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.173341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144743 restraints weight = 19985.112| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.30 r_work: 0.3464 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15130 Z= 0.119 Angle : 0.566 8.877 20667 Z= 0.281 Chirality : 0.043 0.185 2490 Planarity : 0.003 0.049 2577 Dihedral : 5.339 59.025 2873 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 17.31 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.21), residues: 1619 helix: 1.22 (0.28), residues: 370 sheet: 0.27 (0.25), residues: 401 loop : -0.75 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 504 TYR 0.019 0.001 TYR A 165 PHE 0.026 0.001 PHE A 53 TRP 0.024 0.001 TRP B 631 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00275 (15054) covalent geometry : angle 0.54845 (20472) SS BOND : bond 0.00340 ( 33) SS BOND : angle 0.89766 ( 66) hydrogen bonds : bond 0.03746 ( 444) hydrogen bonds : angle 4.66491 ( 1167) link_ALPHA1-3 : bond 0.00762 ( 1) link_ALPHA1-3 : angle 1.58879 ( 3) link_BETA1-4 : bond 0.00430 ( 9) link_BETA1-4 : angle 1.65575 ( 27) link_NAG-ASN : bond 0.00245 ( 33) link_NAG-ASN : angle 1.81394 ( 99) ********************** 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 313 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 287 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8526 (mmm) cc_final: 0.6879 (mmt) REVERT: A 153 MET cc_start: 0.8183 (ttm) cc_final: 0.7886 (ttm) REVERT: A 265 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8715 (mp) REVERT: A 302 ASN cc_start: 0.9050 (m-40) cc_final: 0.8799 (t0) REVERT: A 434 MET cc_start: 0.9199 (ttp) cc_final: 0.8930 (ttm) REVERT: A 500 ARG cc_start: 0.6351 (ttt-90) cc_final: 0.6088 (ttt-90) REVERT: C 540 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.6798 (mp10) REVERT: C 588 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6305 (tmm-80) REVERT: C 634 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8424 (mt-10) REVERT: E 114 GLN cc_start: 0.8441 (tt0) cc_final: 0.8145 (tt0) REVERT: E 140 ASP cc_start: 0.7009 (m-30) cc_final: 0.6628 (t0) REVERT: E 156 GLU cc_start: 0.7694 (mp0) cc_final: 0.6954 (mt-10) REVERT: E 233 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.5876 (p90) REVERT: E 432 GLN cc_start: 0.8395 (mp10) cc_final: 0.8133 (mp10) REVERT: D 543 ASN cc_start: 0.8285 (m-40) cc_final: 0.7967 (m110) REVERT: D 585 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8483 (mtm-85) REVERT: D 626 MET cc_start: 0.6608 (ptt) cc_final: 0.6388 (ptp) REVERT: F 160 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7562 (tptp) REVERT: F 316 TRP cc_start: 0.8229 (m100) cc_final: 0.7892 (m100) REVERT: F 486 TYR cc_start: 0.8850 (m-80) cc_final: 0.8289 (m-10) outliers start: 26 outliers final: 22 residues processed: 304 average time/residue: 0.1335 time to fit residues: 59.4806 Evaluate side-chains 303 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 278 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 326 ILE 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 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 106 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 146 optimal weight: 6.9990 chunk 8 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.172066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143385 restraints weight = 20035.756| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.28 r_work: 0.3457 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15130 Z= 0.133 Angle : 0.573 8.984 20667 Z= 0.285 Chirality : 0.043 0.186 2490 Planarity : 0.003 0.054 2577 Dihedral : 5.327 55.280 2873 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.04 % Allowed : 16.77 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.21), residues: 1619 helix: 1.20 (0.29), residues: 370 sheet: 0.24 (0.25), residues: 401 loop : -0.76 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 617 TYR 0.019 0.001 TYR A 165 PHE 0.025 0.002 PHE A 53 TRP 0.023 0.001 TRP B 631 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00310 (15054) covalent geometry : angle 0.55600 (20472) SS BOND : bond 0.00348 ( 33) SS BOND : angle 0.91722 ( 66) hydrogen bonds : bond 0.03801 ( 444) hydrogen bonds : angle 4.68643 ( 1167) link_ALPHA1-3 : bond 0.00770 ( 1) link_ALPHA1-3 : angle 1.65423 ( 3) link_BETA1-4 : bond 0.00418 ( 9) link_BETA1-4 : angle 1.69232 ( 27) link_NAG-ASN : bond 0.00247 ( 33) link_NAG-ASN : angle 1.81626 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4119.99 seconds wall clock time: 71 minutes 39.69 seconds (4299.69 seconds total)