Starting phenix.real_space_refine on Sat Mar 16 06:07:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/03_2024/6itc_9731_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/03_2024/6itc_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_9731/03_2024/6itc_9731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/03_2024/6itc_9731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/03_2024/6itc_9731_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6itc_9731/03_2024/6itc_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.47, per 1000 atoms: 0.61 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 3.0 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: 3.09 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: 4.23 Time building geometry restraints manager: 5.82 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: 0.660 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: 3.620 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 40.780 Find NCS groups from input model: 0.370 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.770 ------------------------------------------------------------------------------- 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 : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8559 (mt) cc_final: 0.8358 (mt) REVERT: A 501 GLU cc_start: 0.8076 (mp0) cc_final: 0.7694 (mp0) REVERT: A 539 LEU cc_start: 0.8549 (mm) cc_final: 0.8245 (mp) REVERT: A 543 ASP cc_start: 0.8185 (t70) cc_final: 0.7928 (t0) REVERT: A 549 PHE cc_start: 0.7942 (m-80) cc_final: 0.7604 (m-80) REVERT: A 555 MET cc_start: 0.7244 (mmt) cc_final: 0.6863 (mmm) REVERT: A 601 ASP cc_start: 0.7630 (t0) cc_final: 0.7210 (t0) REVERT: Y 67 PHE cc_start: 0.8333 (t80) cc_final: 0.8024 (t80) REVERT: Y 139 MET cc_start: 0.8134 (pmt) cc_final: 0.7636 (pmt) REVERT: Y 142 GLN cc_start: 0.6868 (pp30) cc_final: 0.6646 (pp30) REVERT: V 64 LYS cc_start: 0.7349 (tptt) cc_final: 0.7090 (tptp) REVERT: V 103 SER cc_start: 0.8691 (m) cc_final: 0.8418 (p) REVERT: G 18 LEU cc_start: 0.7640 (tt) cc_final: 0.7197 (tp) REVERT: G 55 VAL cc_start: 0.7963 (m) cc_final: 0.7731 (p) REVERT: G 123 ILE cc_start: 0.8021 (mp) cc_final: 0.7447 (mp) REVERT: C 81 GLN cc_start: 0.6739 (mm110) cc_final: 0.6291 (mm-40) REVERT: C 98 PHE cc_start: 0.6912 (m-10) cc_final: 0.6615 (m-80) REVERT: C 101 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6681 (tm-30) outliers start: 15 outliers final: 2 residues processed: 427 average time/residue: 0.2768 time to fit residues: 167.0577 Evaluate side-chains 268 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 266 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 602 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 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 17 ASN A 287 ASN A 297 HIS A 359 ASN ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS A 529 GLN A 613 GLN A 747 ASN A 753 GLN Y 101 GLN Y 134 ASN ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7609 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14097 Z= 0.228 Angle : 0.754 9.389 19037 Z= 0.389 Chirality : 0.047 0.288 2129 Planarity : 0.005 0.055 2444 Dihedral : 10.923 161.830 1973 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.93 % Allowed : 13.50 % Favored : 82.56 % 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: -2.84 (0.19), residues: 1719 helix: -1.13 (0.18), residues: 763 sheet: -1.81 (0.27), residues: 316 loop : -2.71 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 103 HIS 0.007 0.001 HIS G 181 PHE 0.034 0.002 PHE Y 276 TYR 0.022 0.002 TYR V 79 ARG 0.005 0.001 ARG A 645 *********************** 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 368 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 310 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8333 (mmm) cc_final: 0.7872 (mmm) REVERT: A 242 ARG cc_start: 0.8055 (ttp-110) cc_final: 0.7853 (ttp-170) REVERT: A 427 MET cc_start: 0.7475 (ppp) cc_final: 0.7200 (ppp) REVERT: A 515 SER cc_start: 0.8746 (t) cc_final: 0.8283 (m) REVERT: A 573 MET cc_start: 0.4780 (tpp) cc_final: 0.4456 (tpt) REVERT: A 601 ASP cc_start: 0.7815 (t0) cc_final: 0.7314 (t0) REVERT: A 733 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8060 (tt0) REVERT: Y 104 MET cc_start: 0.7075 (tpp) cc_final: 0.6479 (mmt) REVERT: V 64 LYS cc_start: 0.7314 (tptt) cc_final: 0.7037 (tptp) REVERT: V 79 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.7243 (m-80) REVERT: G 123 ILE cc_start: 0.7731 (mp) cc_final: 0.7509 (mp) REVERT: G 200 TYR cc_start: 0.6167 (p90) cc_final: 0.5844 (p90) REVERT: C 72 ASP cc_start: 0.7652 (p0) cc_final: 0.7064 (p0) REVERT: C 77 THR cc_start: 0.8035 (m) cc_final: 0.7719 (m) REVERT: C 81 GLN cc_start: 0.6723 (mm110) cc_final: 0.6299 (mm-40) outliers start: 58 outliers final: 29 residues processed: 344 average time/residue: 0.2451 time to fit residues: 123.1791 Evaluate side-chains 289 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 259 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 776 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 79 TYR Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 101 GLN Y 387 ASN B 57 HIS ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 14097 Z= 0.375 Angle : 0.797 9.683 19037 Z= 0.412 Chirality : 0.050 0.254 2129 Planarity : 0.005 0.057 2444 Dihedral : 10.334 169.190 1970 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.29 % Allowed : 15.88 % Favored : 78.83 % 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: -2.38 (0.19), residues: 1719 helix: -0.67 (0.18), residues: 758 sheet: -1.61 (0.27), residues: 312 loop : -2.56 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 103 HIS 0.005 0.001 HIS G 199 PHE 0.041 0.003 PHE Y 276 TYR 0.025 0.002 TYR V 96 ARG 0.005 0.001 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 343 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 265 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8010 (tt) REVERT: A 141 MET cc_start: 0.8893 (mmm) cc_final: 0.8368 (mmm) REVERT: A 212 ILE cc_start: 0.9301 (mm) cc_final: 0.9094 (mt) REVERT: A 347 ASN cc_start: 0.8676 (m-40) cc_final: 0.8468 (m-40) REVERT: A 384 ILE cc_start: 0.9092 (mm) cc_final: 0.8804 (mt) REVERT: A 405 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: A 557 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7847 (mtm) REVERT: A 573 MET cc_start: 0.5342 (tpp) cc_final: 0.5081 (tpt) REVERT: A 645 ARG cc_start: 0.7724 (tmt170) cc_final: 0.7398 (tpt170) REVERT: A 733 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8263 (tt0) REVERT: A 735 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8136 (ttt-90) REVERT: Y 64 LEU cc_start: 0.8078 (mt) cc_final: 0.7707 (mp) REVERT: Y 104 MET cc_start: 0.7114 (tpp) cc_final: 0.6450 (mmt) REVERT: Y 301 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7900 (mtm-85) REVERT: Y 326 TYR cc_start: 0.8610 (t80) cc_final: 0.8330 (t80) REVERT: E 2 GLN cc_start: 0.6737 (mm-40) cc_final: 0.6432 (pp30) REVERT: V 39 GLN cc_start: 0.7677 (pp30) cc_final: 0.7466 (tm-30) REVERT: V 79 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: G 123 ILE cc_start: 0.7754 (mp) cc_final: 0.7111 (mp) REVERT: G 143 TYR cc_start: 0.8276 (t80) cc_final: 0.7597 (t80) REVERT: G 145 TYR cc_start: 0.7023 (t80) cc_final: 0.6816 (t80) REVERT: G 200 TYR cc_start: 0.6474 (p90) cc_final: 0.6115 (p90) REVERT: C 72 ASP cc_start: 0.6718 (p0) cc_final: 0.6513 (p0) REVERT: C 101 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6561 (tm-30) outliers start: 78 outliers final: 48 residues processed: 317 average time/residue: 0.2582 time to fit residues: 120.0532 Evaluate side-chains 297 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 244 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 18 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 264 LEU Chi-restraints excluded: chain Y residue 305 ASP Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 406 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 79 TYR Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 96 VAL 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: 1.9990 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** 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: 0.7816 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14097 Z= 0.248 Angle : 0.686 8.583 19037 Z= 0.353 Chirality : 0.046 0.224 2129 Planarity : 0.004 0.050 2444 Dihedral : 9.667 171.102 1970 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.41 % Allowed : 18.05 % Favored : 77.54 % 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: -1.76 (0.20), residues: 1719 helix: -0.04 (0.19), residues: 746 sheet: -1.44 (0.28), residues: 307 loop : -2.27 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 103 HIS 0.006 0.001 HIS G 181 PHE 0.031 0.002 PHE Y 276 TYR 0.026 0.002 TYR V 96 ARG 0.005 0.000 ARG G 122 *********************** 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 336 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 271 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 141 MET cc_start: 0.8870 (mmm) cc_final: 0.8346 (mmm) REVERT: A 157 ASN cc_start: 0.8086 (t0) cc_final: 0.7776 (t0) REVERT: A 384 ILE cc_start: 0.9191 (mm) cc_final: 0.8922 (mt) REVERT: A 573 MET cc_start: 0.5107 (tpp) cc_final: 0.4875 (tpt) REVERT: A 645 ARG cc_start: 0.7754 (tmt170) cc_final: 0.7516 (tpt170) REVERT: A 659 ASP cc_start: 0.7704 (t70) cc_final: 0.7371 (t0) REVERT: A 733 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8314 (tt0) REVERT: Y 9 MET cc_start: 0.7224 (mmm) cc_final: 0.6913 (mmt) REVERT: Y 64 LEU cc_start: 0.8043 (mt) cc_final: 0.7634 (mp) REVERT: Y 301 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7878 (mtm-85) REVERT: Y 326 TYR cc_start: 0.8504 (t80) cc_final: 0.8266 (t80) REVERT: E 2 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6463 (pp30) REVERT: V 79 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: G 18 LEU cc_start: 0.7655 (tp) cc_final: 0.7074 (tt) REVERT: G 73 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6594 (ttm-80) REVERT: G 200 TYR cc_start: 0.6289 (p90) cc_final: 0.6000 (p90) REVERT: C 56 ARG cc_start: 0.6735 (ptm-80) cc_final: 0.6140 (ptm-80) REVERT: C 98 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: C 101 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6567 (tm-30) REVERT: C 103 TRP cc_start: 0.7799 (m100) cc_final: 0.7361 (m100) outliers start: 65 outliers final: 40 residues processed: 317 average time/residue: 0.2524 time to fit residues: 117.2383 Evaluate side-chains 287 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 244 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 305 ASP Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 79 TYR Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 114 optimal weight: 0.0170 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 101 GLN ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 GLN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14097 Z= 0.248 Angle : 0.681 8.453 19037 Z= 0.347 Chirality : 0.046 0.206 2129 Planarity : 0.004 0.052 2444 Dihedral : 9.146 168.512 1970 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.02 % Allowed : 18.59 % Favored : 76.39 % 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: -1.53 (0.20), residues: 1719 helix: 0.22 (0.20), residues: 746 sheet: -1.39 (0.28), residues: 310 loop : -2.22 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 103 HIS 0.005 0.001 HIS G 169 PHE 0.027 0.002 PHE G 27 TYR 0.026 0.002 TYR V 96 ARG 0.004 0.000 ARG G 122 *********************** 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 327 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 253 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8561 (mp) cc_final: 0.8300 (mp) REVERT: A 141 MET cc_start: 0.8839 (mmm) cc_final: 0.8301 (mmm) REVERT: A 384 ILE cc_start: 0.9204 (mm) cc_final: 0.8955 (mt) REVERT: A 645 ARG cc_start: 0.7768 (tmt170) cc_final: 0.7541 (tpt170) REVERT: A 659 ASP cc_start: 0.7756 (t70) cc_final: 0.7405 (t0) REVERT: Y 104 MET cc_start: 0.6820 (tpp) cc_final: 0.5928 (mmt) REVERT: Y 301 ARG cc_start: 0.8082 (mtm110) cc_final: 0.7848 (mtm-85) REVERT: Y 326 TYR cc_start: 0.8515 (t80) cc_final: 0.8299 (t80) REVERT: E 2 GLN cc_start: 0.6920 (mm-40) cc_final: 0.6442 (pp30) REVERT: V 79 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: V 102 MET cc_start: 0.7104 (pmm) cc_final: 0.6824 (pmm) REVERT: G 73 ARG cc_start: 0.7213 (ttp80) cc_final: 0.6710 (ttm-80) REVERT: G 200 TYR cc_start: 0.6273 (p90) cc_final: 0.6001 (p90) REVERT: G 204 GLN cc_start: 0.7076 (pt0) cc_final: 0.6840 (pt0) REVERT: C 56 ARG cc_start: 0.6751 (ptm-80) cc_final: 0.6153 (ptm-80) REVERT: C 81 GLN cc_start: 0.6558 (mm110) cc_final: 0.6117 (mm-40) REVERT: C 98 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: C 101 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6704 (tm-30) REVERT: C 103 TRP cc_start: 0.7810 (m100) cc_final: 0.7500 (m100) outliers start: 74 outliers final: 52 residues processed: 303 average time/residue: 0.2789 time to fit residues: 124.6894 Evaluate side-chains 286 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 232 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 79 TYR Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14097 Z= 0.273 Angle : 0.686 8.707 19037 Z= 0.350 Chirality : 0.046 0.197 2129 Planarity : 0.004 0.051 2444 Dihedral : 8.764 170.614 1970 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 5.43 % Allowed : 18.93 % Favored : 75.64 % 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: -1.39 (0.20), residues: 1719 helix: 0.31 (0.20), residues: 748 sheet: -1.36 (0.28), residues: 311 loop : -2.09 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 103 HIS 0.005 0.001 HIS G 181 PHE 0.029 0.002 PHE Y 276 TYR 0.028 0.002 TYR V 96 ARG 0.004 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 318 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 238 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8335 (mp) REVERT: A 157 ASN cc_start: 0.8090 (t160) cc_final: 0.7872 (t0) REVERT: A 317 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7091 (m-30) REVERT: A 384 ILE cc_start: 0.9185 (mm) cc_final: 0.8966 (mt) REVERT: A 645 ARG cc_start: 0.7727 (tmt170) cc_final: 0.7526 (tpt170) REVERT: A 659 ASP cc_start: 0.7826 (t70) cc_final: 0.7491 (t0) REVERT: A 735 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8088 (ttt-90) REVERT: Y 104 MET cc_start: 0.6991 (tpp) cc_final: 0.5998 (mmt) REVERT: Y 301 ARG cc_start: 0.8096 (mtm110) cc_final: 0.7864 (mtm-85) REVERT: E 2 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6397 (pp30) REVERT: E 16 LYS cc_start: 0.8358 (mttm) cc_final: 0.7825 (mmmt) REVERT: V 79 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: G 73 ARG cc_start: 0.7226 (ttp80) cc_final: 0.6795 (ttm-80) REVERT: G 200 TYR cc_start: 0.6277 (p90) cc_final: 0.6022 (p90) REVERT: C 101 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6681 (tm-30) REVERT: C 103 TRP cc_start: 0.7864 (m100) cc_final: 0.7497 (m100) outliers start: 80 outliers final: 60 residues processed: 296 average time/residue: 0.2548 time to fit residues: 109.7819 Evaluate side-chains 296 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 232 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 89 MET Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 413 MET Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 79 TYR Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 0.0370 chunk 164 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 76 optimal weight: 10.0000 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 GLN ** G 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14097 Z= 0.218 Angle : 0.665 9.627 19037 Z= 0.337 Chirality : 0.045 0.185 2129 Planarity : 0.004 0.046 2444 Dihedral : 8.386 170.189 1970 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.95 % Allowed : 19.81 % Favored : 75.24 % 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: -1.24 (0.21), residues: 1719 helix: 0.41 (0.20), residues: 754 sheet: -1.26 (0.28), residues: 311 loop : -2.02 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP V 107 HIS 0.005 0.001 HIS G 169 PHE 0.025 0.002 PHE Y 276 TYR 0.030 0.001 TYR V 96 ARG 0.005 0.000 ARG Y 10 *********************** 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 314 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 241 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8313 (mp) REVERT: A 157 ASN cc_start: 0.8090 (t160) cc_final: 0.7883 (t0) REVERT: A 317 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7081 (m-30) REVERT: A 384 ILE cc_start: 0.9195 (mm) cc_final: 0.8975 (mt) REVERT: A 659 ASP cc_start: 0.7795 (t70) cc_final: 0.7582 (t0) REVERT: A 735 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8062 (ttt-90) REVERT: Y 48 ASP cc_start: 0.7335 (m-30) cc_final: 0.7111 (m-30) REVERT: Y 104 MET cc_start: 0.7167 (tpp) cc_final: 0.6120 (mmt) REVERT: Y 217 LEU cc_start: 0.8459 (mt) cc_final: 0.8076 (tt) REVERT: E 2 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6425 (pp30) REVERT: E 16 LYS cc_start: 0.8332 (mttm) cc_final: 0.7820 (mmmt) REVERT: V 45 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6393 (mtm110) REVERT: V 79 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7135 (m-80) REVERT: G 73 ARG cc_start: 0.7205 (ttp80) cc_final: 0.6682 (ttm-80) REVERT: G 200 TYR cc_start: 0.6321 (p90) cc_final: 0.6085 (p90) REVERT: C 101 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6557 (tm-30) REVERT: C 103 TRP cc_start: 0.7910 (m100) cc_final: 0.7536 (m100) outliers start: 73 outliers final: 59 residues processed: 293 average time/residue: 0.2603 time to fit residues: 110.5609 Evaluate side-chains 290 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 226 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 89 MET Chi-restraints excluded: chain Y residue 179 ILE Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 358 GLU Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain V residue 45 ARG Chi-restraints excluded: chain V residue 58 MET Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 79 TYR Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 ASN Y 101 GLN B 57 HIS ** G 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5446 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= 0.223 Angle : 0.669 8.849 19037 Z= 0.339 Chirality : 0.045 0.182 2129 Planarity : 0.004 0.046 2444 Dihedral : 8.200 170.238 1970 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.09 % Allowed : 20.22 % Favored : 74.69 % 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: -1.16 (0.21), residues: 1719 helix: 0.48 (0.20), residues: 755 sheet: -1.16 (0.29), residues: 310 loop : -2.02 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 107 HIS 0.005 0.001 HIS G 181 PHE 0.025 0.002 PHE Y 276 TYR 0.028 0.002 TYR V 96 ARG 0.009 0.000 ARG Y 301 *********************** 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 314 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 239 time to evaluate : 1.843 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: A 384 ILE cc_start: 0.9182 (mm) cc_final: 0.8981 (mt) REVERT: A 659 ASP cc_start: 0.7821 (t70) cc_final: 0.7608 (t0) REVERT: A 735 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8068 (ttt-90) REVERT: Y 50 LEU cc_start: 0.4641 (OUTLIER) cc_final: 0.4321 (mt) REVERT: Y 104 MET cc_start: 0.7383 (tpp) cc_final: 0.6187 (mmt) REVERT: Y 130 TYR cc_start: 0.7467 (t80) cc_final: 0.7214 (t80) REVERT: Y 217 LEU cc_start: 0.8535 (mt) cc_final: 0.8173 (tt) REVERT: E 2 GLN cc_start: 0.6864 (mm-40) cc_final: 0.6397 (pp30) REVERT: E 16 LYS cc_start: 0.8341 (mttm) cc_final: 0.7871 (mmmt) REVERT: V 79 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: V 94 TYR cc_start: 0.7089 (m-80) cc_final: 0.6786 (m-80) REVERT: G 73 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6622 (ttt180) REVERT: G 200 TYR cc_start: 0.6307 (p90) cc_final: 0.6088 (p90) REVERT: C 56 ARG cc_start: 0.6787 (ptm-80) cc_final: 0.5795 (ttp80) REVERT: C 101 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6569 (tm-30) REVERT: C 103 TRP cc_start: 0.7915 (m100) cc_final: 0.7643 (m100) outliers start: 75 outliers final: 62 residues processed: 294 average time/residue: 0.2410 time to fit residues: 103.0587 Evaluate side-chains 297 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 231 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 89 MET Chi-restraints excluded: chain Y residue 101 GLN Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 179 ILE Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 260 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 358 GLU Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain V residue 45 ARG Chi-restraints excluded: chain V residue 58 MET Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 79 TYR Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 144 optimal weight: 0.2980 chunk 153 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 GLN ** Y 261 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14097 Z= 0.303 Angle : 0.710 10.942 19037 Z= 0.360 Chirality : 0.047 0.202 2129 Planarity : 0.004 0.045 2444 Dihedral : 8.234 171.010 1970 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.09 % Allowed : 20.35 % Favored : 74.56 % 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: -1.26 (0.21), residues: 1719 helix: 0.35 (0.19), residues: 759 sheet: -1.13 (0.29), residues: 310 loop : -2.07 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP V 107 HIS 0.004 0.001 HIS G 181 PHE 0.032 0.002 PHE Y 276 TYR 0.026 0.002 TYR G 106 ARG 0.007 0.000 ARG Y 301 *********************** 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 309 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 234 time to evaluate : 1.660 Fit side-chains REVERT: A 317 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7156 (m-30) REVERT: A 555 MET cc_start: 0.7012 (mmp) cc_final: 0.6655 (mmm) REVERT: A 659 ASP cc_start: 0.7865 (t70) cc_final: 0.7649 (t0) REVERT: A 735 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8082 (ttt-90) REVERT: Y 9 MET cc_start: 0.7254 (mmp) cc_final: 0.6983 (mmt) REVERT: Y 50 LEU cc_start: 0.4694 (OUTLIER) cc_final: 0.4285 (mt) REVERT: Y 130 TYR cc_start: 0.7425 (t80) cc_final: 0.7159 (t80) REVERT: Y 134 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7337 (t0) REVERT: Y 217 LEU cc_start: 0.8547 (mt) cc_final: 0.8191 (tt) REVERT: E 2 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6418 (pp30) REVERT: E 16 LYS cc_start: 0.8362 (mttm) cc_final: 0.7895 (mmmt) REVERT: V 34 MET cc_start: 0.6956 (mmm) cc_final: 0.5721 (mpp) REVERT: V 79 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: V 100 THR cc_start: 0.8820 (t) cc_final: 0.8278 (p) REVERT: G 73 ARG cc_start: 0.7237 (ttp80) cc_final: 0.6782 (ttt180) REVERT: G 145 TYR cc_start: 0.6517 (t80) cc_final: 0.6159 (t80) REVERT: G 200 TYR cc_start: 0.6329 (p90) cc_final: 0.6109 (p90) REVERT: C 81 GLN cc_start: 0.6543 (mm110) cc_final: 0.6083 (mm-40) REVERT: C 101 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6559 (tm-30) REVERT: C 103 TRP cc_start: 0.7950 (m100) cc_final: 0.7654 (m100) outliers start: 75 outliers final: 63 residues processed: 292 average time/residue: 0.2550 time to fit residues: 108.3015 Evaluate side-chains 296 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 228 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 89 MET Chi-restraints excluded: chain Y residue 134 ASN Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 179 ILE Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 260 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 341 LYS Chi-restraints excluded: chain Y residue 358 GLU Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain V residue 45 ARG Chi-restraints excluded: chain V residue 58 MET Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 79 TYR Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 GLN ** Y 261 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5668 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= 0.222 Angle : 0.688 10.528 19037 Z= 0.347 Chirality : 0.045 0.180 2129 Planarity : 0.004 0.046 2444 Dihedral : 8.074 170.670 1970 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.68 % Allowed : 21.23 % Favored : 74.08 % 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: -1.09 (0.21), residues: 1719 helix: 0.51 (0.20), residues: 761 sheet: -1.06 (0.29), residues: 311 loop : -2.01 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP V 107 HIS 0.005 0.001 HIS G 181 PHE 0.024 0.002 PHE Y 276 TYR 0.026 0.002 TYR V 96 ARG 0.007 0.000 ARG Y 301 ********************** 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 304 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 235 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: A 555 MET cc_start: 0.7027 (mmp) cc_final: 0.6713 (mmm) REVERT: A 600 ASP cc_start: 0.7491 (m-30) cc_final: 0.6983 (t70) REVERT: A 659 ASP cc_start: 0.7953 (t70) cc_final: 0.7742 (t0) REVERT: Y 9 MET cc_start: 0.7216 (mmp) cc_final: 0.6920 (mmt) REVERT: Y 50 LEU cc_start: 0.4705 (OUTLIER) cc_final: 0.4416 (mt) REVERT: Y 130 TYR cc_start: 0.7349 (t80) cc_final: 0.7140 (t80) REVERT: Y 134 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7256 (t0) REVERT: Y 217 LEU cc_start: 0.8534 (mt) cc_final: 0.8182 (tt) REVERT: E 2 GLN cc_start: 0.6887 (mm-40) cc_final: 0.6422 (pp30) REVERT: E 13 ARG cc_start: 0.8534 (tpp80) cc_final: 0.8287 (ttp-110) REVERT: E 16 LYS cc_start: 0.8289 (mttm) cc_final: 0.7792 (mmmt) REVERT: V 34 MET cc_start: 0.6939 (mmm) cc_final: 0.5643 (mpp) REVERT: V 79 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7252 (m-80) REVERT: V 100 THR cc_start: 0.8816 (t) cc_final: 0.8231 (p) REVERT: G 73 ARG cc_start: 0.7154 (ttp80) cc_final: 0.6702 (ttt180) REVERT: G 145 TYR cc_start: 0.6542 (t80) cc_final: 0.6319 (t80) REVERT: G 200 TYR cc_start: 0.6310 (p90) cc_final: 0.6106 (p90) REVERT: C 81 GLN cc_start: 0.6554 (mm110) cc_final: 0.6002 (mm-40) REVERT: C 82 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5039 (mt) REVERT: C 101 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6534 (tm-30) outliers start: 69 outliers final: 54 residues processed: 288 average time/residue: 0.2624 time to fit residues: 109.6295 Evaluate side-chains 284 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 225 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 89 MET Chi-restraints excluded: chain Y residue 134 ASN Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 179 ILE Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 260 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 341 LYS Chi-restraints excluded: chain Y residue 358 GLU Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 79 TYR Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 119 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Y 101 GLN ** Y 261 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.157535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121140 restraints weight = 22967.810| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.90 r_work: 0.3181 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 0.036 14097 Z= 0.183 Angle : 0.671 10.241 19037 Z= 0.338 Chirality : 0.044 0.172 2129 Planarity : 0.004 0.047 2444 Dihedral : 7.835 168.582 1970 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.93 % Allowed : 22.25 % Favored : 73.81 % 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: -0.91 (0.21), residues: 1719 helix: 0.69 (0.20), residues: 760 sheet: -0.95 (0.29), residues: 311 loop : -1.96 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 103 HIS 0.005 0.001 HIS G 181 PHE 0.022 0.002 PHE E 39 TYR 0.026 0.001 TYR V 96 ARG 0.007 0.000 ARG Y 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3293.24 seconds wall clock time: 61 minutes 35.82 seconds (3695.82 seconds total)