Starting phenix.real_space_refine on Sun Dec 10 08:11:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/12_2023/6itc_9731_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/12_2023/6itc_9731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/12_2023/6itc_9731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/12_2023/6itc_9731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/12_2023/6itc_9731_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/12_2023/6itc_9731_updated.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 64 5.16 5 Be 1 3.05 5 C 8811 2.51 5 N 2365 2.21 5 O 2595 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 624": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ASP 667": "OD1" <-> "OD2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A ARG 750": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 248": "NH1" <-> "NH2" Residue "Y PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 423": "NH1" <-> "NH2" Residue "Y PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "V TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 168": "NH1" <-> "NH2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13844 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6107 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 15, 'TRANS': 749} Chain: "Y" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3275 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "V" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 312 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain breaks: 1 Chain: "G" Number of atoms: 1802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1799 Unusual residues: {'GYS': 1} Classifications: {'peptide': 224, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 212, None: 2} Not linked: pdbres="PHE G 64 " pdbres="GYS G 66 " Not linked: pdbres="GYS G 66 " pdbres="VAL G 68 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GYS:plan-3': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 225, 1799 Unusual residues: {'GYS': 1} Classifications: {'peptide': 224, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 212, None: 2} Not linked: pdbres="PHE G 64 " pdbres="GYS G 66 " Not linked: pdbres="GYS G 66 " pdbres="VAL G 68 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GYS:plan-3': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1836 Chain: "C" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 868 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'PGV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1, 'PGV:plan-1': 1} Unresolved non-hydrogen planarities: 8 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N SER V 25 " occ=0.09 ... (4 atoms not shown) pdb=" OG SER V 25 " occ=0.09 residue: pdb=" N LYS V 86 " occ=0.84 ... (3 atoms not shown) pdb=" CB LYS V 86 " occ=0.84 residue: pdb=" N CYS V 95 " occ=0.93 ... (4 atoms not shown) pdb=" SG CYS V 95 " occ=0.93 Time building chain proxies: 8.70, per 1000 atoms: 0.63 Number of scatterers: 13844 At special positions: 0 Unit cell: (128.1, 99.75, 155.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 64 16.00 P 4 15.00 Mg 1 11.99 F 3 9.00 O 2595 8.00 N 2365 7.00 C 8811 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS Y 60 " - pdb=" SG CYS B 29 " distance=2.06 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=1, symmetry=0 Simple link: pdb=" C PHE G 64 " - pdb=" N GYS G 66 " Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.33 Conformation dependent library (CDL) restraints added in 2.6 seconds 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 13 sheets defined 43.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.634A pdb=" N ARG A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 52 Processing helix chain 'A' and resid 62 through 77 removed outlier: 3.787A pdb=" N THR A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 107 through 117 removed outlier: 3.658A pdb=" N THR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 131 through 146 removed outlier: 4.921A pdb=" N LYS A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.694A pdb=" N THR A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 removed outlier: 3.669A pdb=" N VAL A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 357 through 363 removed outlier: 4.377A pdb=" N MET A 363 " --> pdb=" O ASN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 5.793A pdb=" N GLU A 379 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 464 through 473 removed outlier: 6.004A pdb=" N ALA A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE A 471 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 572 through 618 removed outlier: 4.915A pdb=" N VAL A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 642 removed outlier: 3.980A pdb=" N ARG A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 673 through 675 No H-bonds generated for 'chain 'A' and resid 673 through 675' Processing helix chain 'A' and resid 681 through 703 removed outlier: 4.603A pdb=" N ARG A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 742 removed outlier: 4.166A pdb=" N GLN A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 737 " --> pdb=" O GLN A 733 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N HIS A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU A 740 " --> pdb=" O GLN A 736 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG A 741 " --> pdb=" O GLY A 737 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA A 742 " --> pdb=" O ILE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 776 Processing helix chain 'Y' and resid 5 through 8 No H-bonds generated for 'chain 'Y' and resid 5 through 8' Processing helix chain 'Y' and resid 12 through 30 Processing helix chain 'Y' and resid 41 through 46 Processing helix chain 'Y' and resid 75 through 88 Processing helix chain 'Y' and resid 93 through 101 Processing helix chain 'Y' and resid 103 through 134 removed outlier: 3.868A pdb=" N LYS Y 108 " --> pdb=" O MET Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 172 Processing helix chain 'Y' and resid 178 through 201 removed outlier: 3.774A pdb=" N SER Y 189 " --> pdb=" O ALA Y 185 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLY Y 190 " --> pdb=" O GLY Y 186 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE Y 191 " --> pdb=" O ILE Y 187 " (cutoff:3.500A) Proline residue: Y 192 - end of helix Processing helix chain 'Y' and resid 215 through 235 Processing helix chain 'Y' and resid 272 through 288 Proline residue: Y 284 - end of helix Processing helix chain 'Y' and resid 295 through 303 removed outlier: 3.742A pdb=" N TRP Y 299 " --> pdb=" O ASP Y 295 " (cutoff:3.500A) Processing helix chain 'Y' and resid 311 through 330 Processing helix chain 'Y' and resid 333 through 342 Processing helix chain 'Y' and resid 355 through 389 removed outlier: 4.734A pdb=" N VAL Y 370 " --> pdb=" O ARG Y 366 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY Y 371 " --> pdb=" O LEU Y 367 " (cutoff:3.500A) Proline residue: Y 382 - end of helix removed outlier: 4.143A pdb=" N PHE Y 388 " --> pdb=" O PHE Y 384 " (cutoff:3.500A) Processing helix chain 'Y' and resid 399 through 423 removed outlier: 4.626A pdb=" N ILE Y 404 " --> pdb=" O SER Y 401 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL Y 406 " --> pdb=" O LEU Y 403 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY Y 407 " --> pdb=" O ILE Y 404 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL Y 408 " --> pdb=" O VAL Y 405 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU Y 410 " --> pdb=" O GLY Y 407 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU Y 411 " --> pdb=" O VAL Y 408 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR Y 412 " --> pdb=" O ALA Y 409 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS Y 414 " --> pdb=" O GLU Y 411 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN Y 415 " --> pdb=" O THR Y 412 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER Y 418 " --> pdb=" O GLN Y 415 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL Y 421 " --> pdb=" O SER Y 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 16 removed outlier: 4.276A pdb=" N LYS E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 58 removed outlier: 4.138A pdb=" N LEU E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 89 No H-bonds generated for 'chain 'V' and resid 87 through 89' Processing helix chain 'B' and resid 3 through 23 removed outlier: 3.971A pdb=" N LEU B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 61 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing sheet with id= A, first strand: chain 'A' and resid 97 through 99 Processing sheet with id= B, first strand: chain 'A' and resid 173 through 176 Processing sheet with id= C, first strand: chain 'A' and resid 306 through 309 Processing sheet with id= D, first strand: chain 'A' and resid 506 through 508 removed outlier: 6.309A pdb=" N GLN A 457 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 220 through 227 removed outlier: 5.977A pdb=" N GLY A 225 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N THR A 351 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA A 227 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER A 349 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'Y' and resid 238 through 242 Processing sheet with id= G, first strand: chain 'V' and resid 4 through 7 Processing sheet with id= H, first strand: chain 'V' and resid 91 through 94 Processing sheet with id= I, first strand: chain 'V' and resid 34 through 37 Processing sheet with id= J, first strand: chain 'G' and resid 25 through 35 removed outlier: 5.932A pdb=" N LEU G 119 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLU G 17 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN G 121 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP G 19 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE G 123 " --> pdb=" O ASP G 19 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP G 21 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU G 125 " --> pdb=" O ASP G 21 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS G 166 " --> pdb=" O ASN G 149 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASN G 149 " --> pdb=" O LYS G 166 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'C' and resid 107 through 109 removed outlier: 3.749A pdb=" N MET C 34 " --> pdb=" O MET C 51 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 50 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 58 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 94 through 96 657 hydrogen bonds defined for protein. 1835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2988 1.32 - 1.45: 3203 1.45 - 1.57: 7774 1.57 - 1.69: 9 1.69 - 1.81: 123 Bond restraints: 14097 Sorted by residual: bond pdb=" BE BEF A1002 " pdb=" F3 BEF A1002 " ideal model delta sigma weight residual 1.476 1.769 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" BE BEF A1002 " pdb=" F1 BEF A1002 " ideal model delta sigma weight residual 1.476 1.761 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" BE BEF A1002 " pdb=" F2 BEF A1002 " ideal model delta sigma weight residual 1.476 1.756 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C19 PGV Y 502 " pdb=" O03 PGV Y 502 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C19 PGV Y 501 " pdb=" O03 PGV Y 501 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 14092 not shown) Histogram of bond angle deviations from ideal: 93.64 - 102.24: 71 102.24 - 110.84: 4482 110.84 - 119.43: 7612 119.43 - 128.03: 6769 128.03 - 136.62: 103 Bond angle restraints: 19037 Sorted by residual: angle pdb=" C GLN Y 65 " pdb=" CA GLN Y 65 " pdb=" CB GLN Y 65 " ideal model delta sigma weight residual 111.22 100.53 10.69 1.23e+00 6.61e-01 7.56e+01 angle pdb=" N LEU A 666 " pdb=" CA LEU A 666 " pdb=" C LEU A 666 " ideal model delta sigma weight residual 110.88 120.21 -9.33 1.28e+00 6.10e-01 5.31e+01 angle pdb=" N GLU A 668 " pdb=" CA GLU A 668 " pdb=" CB GLU A 668 " ideal model delta sigma weight residual 110.80 100.14 10.66 1.49e+00 4.50e-01 5.12e+01 angle pdb=" C ILE Y 275 " pdb=" N PHE Y 276 " pdb=" CA PHE Y 276 " ideal model delta sigma weight residual 122.38 110.27 12.11 1.81e+00 3.05e-01 4.48e+01 angle pdb=" N GLY Y 251 " pdb=" CA GLY Y 251 " pdb=" C GLY Y 251 " ideal model delta sigma weight residual 115.36 124.00 -8.64 1.33e+00 5.65e-01 4.22e+01 ... (remaining 19032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 8348 35.31 - 70.62: 121 70.62 - 105.93: 4 105.93 - 141.24: 2 141.24 - 176.54: 5 Dihedral angle restraints: 8480 sinusoidal: 3474 harmonic: 5006 Sorted by residual: dihedral pdb=" CA VAL V 101 " pdb=" C VAL V 101 " pdb=" N MET V 102 " pdb=" CA MET V 102 " ideal model delta harmonic sigma weight residual -180.00 -112.12 -67.88 0 5.00e+00 4.00e-02 1.84e+02 dihedral pdb=" CA GLY V 42 " pdb=" C GLY V 42 " pdb=" N LYS V 43 " pdb=" CA LYS V 43 " ideal model delta harmonic sigma weight residual -180.00 -133.68 -46.32 0 5.00e+00 4.00e-02 8.58e+01 dihedral pdb=" CA ARG V 44 " pdb=" C ARG V 44 " pdb=" N ARG V 45 " pdb=" CA ARG V 45 " ideal model delta harmonic sigma weight residual -180.00 -138.29 -41.71 0 5.00e+00 4.00e-02 6.96e+01 ... (remaining 8477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1844 0.118 - 0.237: 261 0.237 - 0.355: 17 0.355 - 0.474: 5 0.474 - 0.592: 2 Chirality restraints: 2129 Sorted by residual: chirality pdb=" CA ARG Y 252 " pdb=" N ARG Y 252 " pdb=" C ARG Y 252 " pdb=" CB ARG Y 252 " both_signs ideal model delta sigma weight residual False 2.51 3.10 -0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CA GLU Y 250 " pdb=" N GLU Y 250 " pdb=" C GLU Y 250 " pdb=" CB GLU Y 250 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.35e+00 chirality pdb=" CA ASN C 82A" pdb=" N ASN C 82A" pdb=" C ASN C 82A" pdb=" CB ASN C 82A" both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 2126 not shown) Planarity restraints: 2445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 64 " -0.071 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C PHE G 64 " 0.241 2.00e-02 2.50e+03 pdb=" O PHE G 64 " -0.097 2.00e-02 2.50e+03 pdb=" N GYS G 66 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG V 44 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ARG V 44 " -0.070 2.00e-02 2.50e+03 pdb=" O ARG V 44 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG V 45 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 290 " 0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ILE A 290 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE A 290 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 291 " 0.019 2.00e-02 2.50e+03 ... (remaining 2442 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 7 2.24 - 2.90: 5522 2.90 - 3.57: 19630 3.57 - 4.23: 31743 4.23 - 4.90: 54214 Nonbonded interactions: 111116 Sorted by model distance: nonbonded pdb=" NH2 ARG A 528 " pdb=" F1 BEF A1002 " model vdw 1.574 2.470 nonbonded pdb=" O ASN A 662 " pdb=" O ASP A 667 " model vdw 1.787 3.040 nonbonded pdb=" NH2 ARG A 525 " pdb=" F2 BEF A1002 " model vdw 1.823 2.470 nonbonded pdb=" NZ LYS Y 354 " pdb=" OE2 GLU Y 358 " model vdw 1.882 2.520 nonbonded pdb=" O GLN Y 65 " pdb=" CD GLN Y 65 " model vdw 2.045 3.270 ... (remaining 111111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 3.680 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 39.550 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.016 0.293 14097 Z= 1.010 Angle : 1.483 18.015 19037 Z= 0.793 Chirality : 0.083 0.592 2129 Planarity : 0.009 0.072 2444 Dihedral : 13.871 176.545 5264 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.96 % Favored : 90.92 % Rotamer: Outliers : 1.02 % Allowed : 7.12 % Favored : 91.86 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.16), residues: 1719 helix: -2.86 (0.13), residues: 776 sheet: -1.95 (0.28), residues: 286 loop : -3.14 (0.20), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP G 57 HIS 0.026 0.004 HIS Y 424 PHE 0.049 0.006 PHE A 203 TYR 0.051 0.005 TYR A 174 ARG 0.022 0.002 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 417 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 427 average time/residue: 0.2763 time to fit residues: 167.9380 Evaluate side-chains 258 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 256 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1531 time to fit residues: 2.7112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 287 ASN A 297 HIS A 359 ASN A 513 HIS A 529 GLN A 613 GLN A 747 ASN A 753 GLN Y 101 GLN Y 134 ASN ** Y 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 267 ASN Y 308 HIS Y 355 ASN Y 424 HIS G 25 HIS G 184 GLN ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS C 76 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14097 Z= 0.283 Angle : 0.784 9.628 19037 Z= 0.405 Chirality : 0.048 0.284 2129 Planarity : 0.006 0.054 2444 Dihedral : 10.989 161.729 1969 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 4.41 % Allowed : 13.77 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.19), residues: 1719 helix: -1.21 (0.18), residues: 763 sheet: -1.79 (0.27), residues: 315 loop : -2.72 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 103 HIS 0.007 0.001 HIS G 181 PHE 0.036 0.002 PHE Y 276 TYR 0.022 0.002 TYR V 96 ARG 0.006 0.001 ARG G 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 305 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 33 residues processed: 340 average time/residue: 0.2595 time to fit residues: 129.7418 Evaluate side-chains 280 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 247 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1596 time to fit residues: 11.3962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 53 optimal weight: 0.0470 chunk 124 optimal weight: 6.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 101 GLN Y 142 GLN Y 143 ASN B 57 HIS ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14097 Z= 0.284 Angle : 0.733 10.257 19037 Z= 0.379 Chirality : 0.048 0.254 2129 Planarity : 0.005 0.047 2444 Dihedral : 10.092 169.355 1969 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.65 % Allowed : 17.10 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.19), residues: 1719 helix: -0.44 (0.19), residues: 750 sheet: -1.53 (0.27), residues: 307 loop : -2.46 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 103 HIS 0.006 0.001 HIS G 181 PHE 0.032 0.002 PHE Y 276 TYR 0.024 0.002 TYR V 96 ARG 0.005 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 280 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 303 average time/residue: 0.2745 time to fit residues: 120.1310 Evaluate side-chains 271 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1927 time to fit residues: 9.7478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 156 optimal weight: 0.4980 chunk 165 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 GLN ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN B 57 HIS ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14097 Z= 0.199 Angle : 0.671 7.944 19037 Z= 0.344 Chirality : 0.045 0.223 2129 Planarity : 0.004 0.051 2444 Dihedral : 9.353 170.871 1969 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.17 % Allowed : 18.25 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.20), residues: 1719 helix: 0.07 (0.20), residues: 748 sheet: -1.36 (0.28), residues: 318 loop : -2.24 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 103 HIS 0.007 0.001 HIS G 181 PHE 0.024 0.002 PHE Y 276 TYR 0.024 0.002 TYR V 96 ARG 0.009 0.000 ARG Y 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 274 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 290 average time/residue: 0.2678 time to fit residues: 114.3999 Evaluate side-chains 256 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 242 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1403 time to fit residues: 5.8201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 0.0570 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Y 101 GLN Y 177 ASN Y 357 GLN V 39 GLN V 76 ASN ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14097 Z= 0.194 Angle : 0.665 9.114 19037 Z= 0.340 Chirality : 0.045 0.260 2129 Planarity : 0.004 0.051 2444 Dihedral : 8.845 171.999 1969 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.31 % Allowed : 20.15 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.20), residues: 1719 helix: 0.30 (0.20), residues: 750 sheet: -1.30 (0.28), residues: 308 loop : -2.16 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 103 HIS 0.006 0.001 HIS G 181 PHE 0.024 0.002 PHE Y 276 TYR 0.027 0.002 TYR V 96 ARG 0.005 0.000 ARG Y 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 264 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 288 average time/residue: 0.2595 time to fit residues: 109.1416 Evaluate side-chains 246 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 231 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1671 time to fit residues: 6.4012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Y 101 GLN Y 177 ASN Y 387 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14097 Z= 0.272 Angle : 0.695 8.905 19037 Z= 0.354 Chirality : 0.046 0.217 2129 Planarity : 0.004 0.050 2444 Dihedral : 8.627 172.302 1969 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.97 % Allowed : 21.37 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1719 helix: 0.32 (0.20), residues: 748 sheet: -1.24 (0.28), residues: 316 loop : -2.07 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 103 HIS 0.005 0.001 HIS G 199 PHE 0.031 0.002 PHE Y 276 TYR 0.026 0.002 TYR V 96 ARG 0.005 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 249 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 266 average time/residue: 0.2526 time to fit residues: 98.0584 Evaluate side-chains 249 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 233 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1369 time to fit residues: 5.4729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Y 66 ASN Y 101 GLN ** G 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14097 Z= 0.216 Angle : 0.665 9.203 19037 Z= 0.339 Chirality : 0.045 0.202 2129 Planarity : 0.004 0.046 2444 Dihedral : 8.304 172.684 1969 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.83 % Allowed : 21.64 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1719 helix: 0.44 (0.20), residues: 748 sheet: -1.18 (0.28), residues: 309 loop : -1.97 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 103 HIS 0.005 0.001 HIS G 181 PHE 0.025 0.002 PHE Y 276 TYR 0.030 0.002 TYR V 96 ARG 0.004 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 253 time to evaluate : 1.654 Fit side-chains outliers start: 27 outliers final: 10 residues processed: 272 average time/residue: 0.2657 time to fit residues: 105.4947 Evaluate side-chains 240 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 230 time to evaluate : 1.411 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1335 time to fit residues: 4.4319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0030 chunk 104 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 101 GLN V 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14097 Z= 0.201 Angle : 0.662 8.087 19037 Z= 0.339 Chirality : 0.045 0.191 2129 Planarity : 0.004 0.046 2444 Dihedral : 8.074 171.897 1969 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.02 % Allowed : 22.18 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1719 helix: 0.54 (0.20), residues: 753 sheet: -0.91 (0.29), residues: 292 loop : -1.96 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 103 HIS 0.005 0.001 HIS G 181 PHE 0.024 0.001 PHE Y 276 TYR 0.027 0.002 TYR G 106 ARG 0.004 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 250 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 259 average time/residue: 0.2859 time to fit residues: 106.8667 Evaluate side-chains 243 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 236 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1453 time to fit residues: 4.0676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS Y 101 GLN Y 424 HIS V 39 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14097 Z= 0.203 Angle : 0.664 9.354 19037 Z= 0.338 Chirality : 0.045 0.179 2129 Planarity : 0.004 0.059 2444 Dihedral : 7.946 171.371 1969 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.09 % Allowed : 22.86 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1719 helix: 0.63 (0.20), residues: 753 sheet: -0.83 (0.30), residues: 291 loop : -1.91 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 103 HIS 0.005 0.001 HIS G 181 PHE 0.025 0.002 PHE Y 276 TYR 0.026 0.002 TYR V 96 ARG 0.010 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 246 time to evaluate : 1.650 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 257 average time/residue: 0.2833 time to fit residues: 105.0826 Evaluate side-chains 244 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 235 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1377 time to fit residues: 4.5496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 170 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN Y 101 GLN ** G 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14097 Z= 0.194 Angle : 0.674 10.245 19037 Z= 0.340 Chirality : 0.045 0.169 2129 Planarity : 0.004 0.062 2444 Dihedral : 7.762 170.985 1969 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.41 % Allowed : 23.13 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.21), residues: 1719 helix: 0.66 (0.20), residues: 753 sheet: -0.78 (0.30), residues: 291 loop : -1.84 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 103 HIS 0.005 0.001 HIS G 181 PHE 0.024 0.001 PHE Y 276 TYR 0.027 0.001 TYR V 96 ARG 0.007 0.000 ARG Y 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 1.495 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 249 average time/residue: 0.2753 time to fit residues: 99.0346 Evaluate side-chains 242 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1611 time to fit residues: 3.0777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** 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 = 0.3943 r_free = 0.3943 target = 0.156201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120596 restraints weight = 23191.169| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.87 r_work: 0.3181 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14097 Z= 0.196 Angle : 0.677 13.694 19037 Z= 0.341 Chirality : 0.045 0.207 2129 Planarity : 0.004 0.060 2444 Dihedral : 7.666 170.569 1969 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.54 % Allowed : 23.34 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1719 helix: 0.59 (0.20), residues: 768 sheet: -0.71 (0.30), residues: 281 loop : -1.79 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 103 HIS 0.005 0.001 HIS G 181 PHE 0.025 0.002 PHE Y 276 TYR 0.026 0.002 TYR V 96 ARG 0.007 0.000 ARG Y 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3262.32 seconds wall clock time: 62 minutes 21.61 seconds (3741.61 seconds total)