Starting phenix.real_space_refine on Wed Feb 14 07:48:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfi_31955/02_2024/7vfi_31955.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfi_31955/02_2024/7vfi_31955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfi_31955/02_2024/7vfi_31955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfi_31955/02_2024/7vfi_31955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfi_31955/02_2024/7vfi_31955.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfi_31955/02_2024/7vfi_31955.pdb" } resolution = 3.98 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= 0.007 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5719 2.51 5 N 1497 2.21 5 O 1651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 263": "NH1" <-> "NH2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A PHE 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8903 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4366 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 554} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4361 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 554} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 71 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.28, per 1000 atoms: 0.59 Number of scatterers: 8903 At special positions: 0 Unit cell: (68.89, 107.07, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1651 8.00 N 1497 7.00 C 5719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 68.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 214 Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 218 through 266 removed outlier: 3.906A pdb=" N THR A 222 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 removed outlier: 3.911A pdb=" N PHE A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 298 removed outlier: 3.827A pdb=" N LEU A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 321 Processing helix chain 'A' and resid 321 through 370 Proline residue: A 333 - end of helix removed outlier: 4.263A pdb=" N ALA A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.997A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 433 removed outlier: 4.570A pdb=" N LYS A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 480 removed outlier: 3.615A pdb=" N LEU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 591 through 597 removed outlier: 4.198A pdb=" N SER A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.532A pdb=" N VAL A 608 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 623 Processing helix chain 'A' and resid 626 through 630 removed outlier: 3.795A pdb=" N SER A 629 " --> pdb=" O ASP A 626 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 630 " --> pdb=" O GLY A 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 626 through 630' Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 672 through 679 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 180 through 214 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 217 through 267 removed outlier: 4.048A pdb=" N PHE B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 222 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 removed outlier: 4.062A pdb=" N PHE B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 321 removed outlier: 5.191A pdb=" N ASP B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 370 Proline residue: B 333 - end of helix removed outlier: 4.244A pdb=" N THR B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 4.443A pdb=" N VAL B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 433 removed outlier: 3.907A pdb=" N LEU B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 473 removed outlier: 3.689A pdb=" N LEU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 549 Processing helix chain 'B' and resid 570 through 578 Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 604 through 615 removed outlier: 4.088A pdb=" N VAL B 608 " --> pdb=" O PRO B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 640 through 654 Processing helix chain 'B' and resid 672 through 681 removed outlier: 3.628A pdb=" N LEU B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 700 removed outlier: 3.721A pdb=" N THR B 699 " --> pdb=" O ARG B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.860A pdb=" N ALA B 725 " --> pdb=" O GLN B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 738 removed outlier: 3.716A pdb=" N MET B 738 " --> pdb=" O VAL B 734 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.950A pdb=" N VAL A 500 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 501 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 560 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 661 through 663 removed outlier: 6.705A pdb=" N THR A 531 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A 708 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 516 through 521 removed outlier: 6.073A pdb=" N PHE B 507 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN B 519 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 505 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B 521 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU B 503 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASN B 504 " --> pdb=" O ARG B 558 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG B 558 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 506 " --> pdb=" O GLY B 556 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY B 556 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 530 through 532 Processing sheet with id=AA5, first strand: chain 'B' and resid 560 through 561 Processing sheet with id=AA6, first strand: chain 'B' and resid 708 through 709 removed outlier: 7.046A pdb=" N VAL B 708 " --> pdb=" O VAL B 715 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2708 1.34 - 1.45: 1428 1.45 - 1.57: 4869 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 9069 Sorted by residual: bond pdb=" CAY Y01 A 801 " pdb=" OAG Y01 A 801 " ideal model delta sigma weight residual 1.207 1.431 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" CAY Y01 B 802 " pdb=" OAG Y01 B 802 " ideal model delta sigma weight residual 1.207 1.430 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CAY Y01 B 801 " pdb=" OAG Y01 B 801 " ideal model delta sigma weight residual 1.207 1.430 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CAI Y01 B 802 " pdb=" CAZ Y01 B 802 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.64e+01 bond pdb=" CAI Y01 A 801 " pdb=" CAZ Y01 A 801 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.39e+01 ... (remaining 9064 not shown) Histogram of bond angle deviations from ideal: 95.66 - 103.30: 87 103.30 - 110.94: 3305 110.94 - 118.58: 3960 118.58 - 126.22: 4887 126.22 - 133.86: 81 Bond angle restraints: 12320 Sorted by residual: angle pdb=" N GLU B 448 " pdb=" CA GLU B 448 " pdb=" C GLU B 448 " ideal model delta sigma weight residual 111.28 103.47 7.81 1.09e+00 8.42e-01 5.13e+01 angle pdb=" CAK Y01 B 801 " pdb=" CAI Y01 B 801 " pdb=" CAZ Y01 B 801 " ideal model delta sigma weight residual 124.96 108.20 16.76 3.00e+00 1.11e-01 3.12e+01 angle pdb=" CAM Y01 B 801 " pdb=" CAY Y01 B 801 " pdb=" OAG Y01 B 801 " ideal model delta sigma weight residual 125.42 108.67 16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" CAM Y01 B 802 " pdb=" CAY Y01 B 802 " pdb=" OAG Y01 B 802 " ideal model delta sigma weight residual 125.42 108.75 16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" CAK Y01 A 801 " pdb=" CAI Y01 A 801 " pdb=" CAZ Y01 A 801 " ideal model delta sigma weight residual 124.96 109.89 15.07 3.00e+00 1.11e-01 2.52e+01 ... (remaining 12315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4881 17.13 - 34.26: 484 34.26 - 51.39: 131 51.39 - 68.52: 31 68.52 - 85.65: 13 Dihedral angle restraints: 5540 sinusoidal: 2226 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE B 200 " pdb=" C PHE B 200 " pdb=" N LEU B 201 " pdb=" CA LEU B 201 " ideal model delta harmonic sigma weight residual -180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL A 228 " pdb=" C VAL A 228 " pdb=" N CYS A 229 " pdb=" CA CYS A 229 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA MET A 218 " pdb=" C MET A 218 " pdb=" N ASP A 219 " pdb=" CA ASP A 219 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1382 0.107 - 0.214: 78 0.214 - 0.321: 3 0.321 - 0.428: 0 0.428 - 0.535: 1 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CBE Y01 B 802 " pdb=" CAP Y01 B 802 " pdb=" CBB Y01 B 802 " pdb=" CBI Y01 B 802 " both_signs ideal model delta sigma weight residual False 2.57 2.03 0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CA ARG C 116 " pdb=" N ARG C 116 " pdb=" C ARG C 116 " pdb=" CB ARG C 116 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CBB Y01 B 802 " pdb=" CAC Y01 B 802 " pdb=" CAO Y01 B 802 " pdb=" CBE Y01 B 802 " both_signs ideal model delta sigma weight residual False 2.58 2.35 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1461 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM Y01 B 801 " 0.114 2.00e-02 2.50e+03 2.14e-01 4.57e+02 pdb=" CAY Y01 B 801 " -0.370 2.00e-02 2.50e+03 pdb=" OAG Y01 B 801 " 0.127 2.00e-02 2.50e+03 pdb=" OAW Y01 B 801 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM Y01 B 802 " -0.116 2.00e-02 2.50e+03 2.12e-01 4.50e+02 pdb=" CAY Y01 B 802 " 0.367 2.00e-02 2.50e+03 pdb=" OAG Y01 B 802 " -0.124 2.00e-02 2.50e+03 pdb=" OAW Y01 B 802 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM Y01 A 801 " 0.112 2.00e-02 2.50e+03 2.05e-01 4.20e+02 pdb=" CAY Y01 A 801 " -0.355 2.00e-02 2.50e+03 pdb=" OAG Y01 A 801 " 0.123 2.00e-02 2.50e+03 pdb=" OAW Y01 A 801 " 0.121 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1533 2.75 - 3.29: 9990 3.29 - 3.83: 15747 3.83 - 4.36: 17022 4.36 - 4.90: 27092 Nonbonded interactions: 71384 Sorted by model distance: nonbonded pdb=" O LEU B 561 " pdb=" OH TYR B 569 " model vdw 2.216 2.440 nonbonded pdb=" O LEU A 561 " pdb=" OH TYR A 569 " model vdw 2.220 2.440 nonbonded pdb=" O THR A 373 " pdb=" OG SER A 376 " model vdw 2.225 2.440 nonbonded pdb=" OG SER B 217 " pdb=" OD1 ASP B 219 " model vdw 2.260 2.440 nonbonded pdb=" O THR B 373 " pdb=" OG SER B 376 " model vdw 2.264 2.440 ... (remaining 71379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 169 through 268 or (resid 269 and (name N or name CA or na \ me C or name O or name CB )) or resid 270 through 329 or (resid 330 and (name N \ or name CA or name C or name O or name CB )) or resid 331 through 669 or (resid \ 670 through 672 and (name N or name CA or name C or name O or name CB )) or resi \ d 673 through 677 or (resid 678 and (name N or name CA or name C or name O or na \ me CB )) or resid 679 through 683 or (resid 684 and (name N or name CA or name C \ or name O or name CB )) or resid 685 through 686 or (resid 687 and (name N or n \ ame CA or name C or name O or name CB )) or resid 688 through 695 or (resid 696 \ and (name N or name CA or name C or name O or name CB )) or resid 697 through 73 \ 5 or (resid 736 through 737 and (name N or name CA or name C or name O or name C \ B )) or resid 738 or resid 801)) selection = (chain 'B' and (resid 169 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 276 or (resid 277 and (name N \ or name CA or name C or name O or name CB )) or resid 278 through 335 or (resid \ 336 through 337 and (name N or name CA or name C or name O or name CB )) or resi \ d 338 through 634 or (resid 635 and (name N or name CA or name C or name O or na \ me CB )) or resid 636 through 645 or (resid 646 and (name N or name CA or name C \ or name O or name CB )) or resid 647 through 665 or (resid 666 through 672 and \ (name N or name CA or name C or name O or name CB )) or resid 673 through 734 or \ (resid 735 through 737 and (name N or name CA or name C or name O or name CB )) \ or resid 738 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.000 Extract box with map and model: 4.080 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.710 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.008 0.224 9069 Z= 0.552 Angle : 1.008 16.757 12320 Z= 0.518 Chirality : 0.055 0.535 1464 Planarity : 0.011 0.214 1553 Dihedral : 15.625 85.647 3414 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.21 % Allowed : 11.75 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.21), residues: 1143 helix: -1.02 (0.17), residues: 710 sheet: -4.19 (0.71), residues: 24 loop : -3.04 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 410 HIS 0.009 0.001 HIS B 487 PHE 0.019 0.002 PHE A 221 TYR 0.018 0.002 TYR B 395 ARG 0.008 0.001 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9182 (m-30) cc_final: 0.8976 (m-30) REVERT: A 352 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8959 (mt-10) REVERT: A 485 MET cc_start: 0.9474 (tpt) cc_final: 0.9269 (tmm) REVERT: A 598 TYR cc_start: 0.8904 (t80) cc_final: 0.8637 (t80) REVERT: A 610 GLU cc_start: 0.9870 (tt0) cc_final: 0.9620 (tp30) REVERT: B 260 CYS cc_start: 0.9551 (t) cc_final: 0.9326 (t) REVERT: B 336 MET cc_start: 0.9199 (mmt) cc_final: 0.8522 (tmm) REVERT: B 466 MET cc_start: 0.8930 (mmm) cc_final: 0.8450 (mmm) REVERT: B 576 ARG cc_start: 0.9452 (ttt-90) cc_final: 0.8557 (tpt90) outliers start: 2 outliers final: 2 residues processed: 153 average time/residue: 0.1591 time to fit residues: 36.5665 Evaluate side-chains 121 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 449 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN A 504 ASN A 520 ASN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN A 645 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 519 GLN B 638 GLN B 722 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9069 Z= 0.216 Angle : 0.638 8.920 12320 Z= 0.333 Chirality : 0.040 0.313 1464 Planarity : 0.004 0.046 1553 Dihedral : 8.515 59.298 1460 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.75 % Allowed : 18.20 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.24), residues: 1143 helix: 0.34 (0.18), residues: 740 sheet: -2.28 (0.66), residues: 44 loop : -2.77 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 410 HIS 0.005 0.001 HIS B 487 PHE 0.020 0.002 PHE A 190 TYR 0.017 0.001 TYR A 395 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 598 TYR cc_start: 0.8800 (t80) cc_final: 0.8339 (t80) REVERT: B 260 CYS cc_start: 0.9492 (t) cc_final: 0.9268 (t) REVERT: B 291 MET cc_start: 0.9553 (tpt) cc_final: 0.8764 (tmm) REVERT: B 336 MET cc_start: 0.9197 (mmt) cc_final: 0.8547 (tmm) REVERT: B 382 GLU cc_start: 0.9512 (mp0) cc_final: 0.9180 (mp0) REVERT: B 466 MET cc_start: 0.8924 (mmm) cc_final: 0.8495 (mmm) REVERT: B 576 ARG cc_start: 0.9423 (ttt-90) cc_final: 0.8650 (tpt90) outliers start: 26 outliers final: 16 residues processed: 143 average time/residue: 0.1523 time to fit residues: 33.5507 Evaluate side-chains 133 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 0.0670 chunk 112 optimal weight: 0.8980 chunk 92 optimal weight: 0.0020 chunk 102 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS A 717 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9069 Z= 0.167 Angle : 0.622 11.293 12320 Z= 0.311 Chirality : 0.041 0.307 1464 Planarity : 0.003 0.050 1553 Dihedral : 8.077 59.825 1460 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.60 % Allowed : 19.79 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1143 helix: 0.82 (0.19), residues: 758 sheet: -1.91 (0.70), residues: 44 loop : -2.68 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 322 HIS 0.002 0.001 HIS A 618 PHE 0.014 0.001 PHE A 620 TYR 0.015 0.001 TYR A 395 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 610 GLU cc_start: 0.9859 (tt0) cc_final: 0.9628 (pt0) REVERT: A 649 MET cc_start: 0.9586 (tmm) cc_final: 0.9075 (ppp) REVERT: B 260 CYS cc_start: 0.9449 (t) cc_final: 0.9212 (t) REVERT: B 291 MET cc_start: 0.9555 (tpt) cc_final: 0.8924 (tmm) REVERT: B 336 MET cc_start: 0.9211 (mmt) cc_final: 0.8563 (tmm) REVERT: B 382 GLU cc_start: 0.9510 (mp0) cc_final: 0.9195 (mp0) REVERT: B 466 MET cc_start: 0.8914 (mmm) cc_final: 0.8506 (mmm) REVERT: B 479 ILE cc_start: 0.9446 (tt) cc_final: 0.9212 (tt) REVERT: B 576 ARG cc_start: 0.9425 (ttt-90) cc_final: 0.8627 (tpt90) REVERT: B 663 ASP cc_start: 0.8474 (t0) cc_final: 0.8210 (t0) outliers start: 34 outliers final: 21 residues processed: 155 average time/residue: 0.1593 time to fit residues: 37.2746 Evaluate side-chains 143 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 632 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9069 Z= 0.201 Angle : 0.623 13.431 12320 Z= 0.315 Chirality : 0.040 0.302 1464 Planarity : 0.003 0.042 1553 Dihedral : 7.798 59.102 1458 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.02 % Allowed : 22.54 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1143 helix: 1.11 (0.19), residues: 744 sheet: -1.82 (0.73), residues: 44 loop : -2.47 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 410 HIS 0.005 0.001 HIS B 487 PHE 0.013 0.001 PHE A 190 TYR 0.017 0.001 TYR A 346 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8849 (m-30) cc_final: 0.8622 (m-30) REVERT: B 260 CYS cc_start: 0.9461 (t) cc_final: 0.9169 (t) REVERT: B 291 MET cc_start: 0.9573 (tpt) cc_final: 0.8885 (tmm) REVERT: B 320 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8922 (mm) REVERT: B 336 MET cc_start: 0.9205 (mmt) cc_final: 0.8582 (tmm) REVERT: B 371 MET cc_start: 0.8838 (ppp) cc_final: 0.8529 (ppp) REVERT: B 466 MET cc_start: 0.8895 (mmm) cc_final: 0.8486 (mmm) REVERT: B 548 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9356 (mm) REVERT: B 576 ARG cc_start: 0.9442 (ttt-90) cc_final: 0.8628 (tpt90) REVERT: B 738 MET cc_start: 0.9274 (pmm) cc_final: 0.8937 (pmm) outliers start: 38 outliers final: 29 residues processed: 145 average time/residue: 0.1465 time to fit residues: 33.0239 Evaluate side-chains 147 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 632 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.0270 chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9069 Z= 0.230 Angle : 0.654 12.512 12320 Z= 0.327 Chirality : 0.040 0.298 1464 Planarity : 0.003 0.038 1553 Dihedral : 7.686 57.754 1458 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.23 % Allowed : 23.92 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1143 helix: 1.18 (0.19), residues: 744 sheet: -2.08 (0.74), residues: 46 loop : -2.27 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 322 HIS 0.005 0.001 HIS B 487 PHE 0.013 0.002 PHE B 387 TYR 0.015 0.001 TYR A 346 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 120 time to evaluate : 1.155 Fit side-chains REVERT: A 274 ASP cc_start: 0.8893 (m-30) cc_final: 0.8610 (m-30) REVERT: A 607 MET cc_start: 0.9668 (ttt) cc_final: 0.9151 (tpt) REVERT: A 610 GLU cc_start: 0.9864 (tt0) cc_final: 0.9652 (pt0) REVERT: A 649 MET cc_start: 0.9619 (tmm) cc_final: 0.9026 (ppp) REVERT: B 260 CYS cc_start: 0.9485 (t) cc_final: 0.9173 (t) REVERT: B 291 MET cc_start: 0.9591 (tpt) cc_final: 0.8860 (tmm) REVERT: B 320 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8931 (mm) REVERT: B 336 MET cc_start: 0.9214 (mmt) cc_final: 0.8603 (tmm) REVERT: B 466 MET cc_start: 0.8882 (mmm) cc_final: 0.8451 (mmm) REVERT: B 485 MET cc_start: 0.9144 (mmt) cc_final: 0.8464 (mmm) REVERT: B 548 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9365 (mm) REVERT: B 576 ARG cc_start: 0.9454 (ttt-90) cc_final: 0.8637 (tpt90) REVERT: B 738 MET cc_start: 0.9314 (pmm) cc_final: 0.9008 (pmm) outliers start: 40 outliers final: 28 residues processed: 142 average time/residue: 0.1523 time to fit residues: 33.3794 Evaluate side-chains 145 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 632 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0570 chunk 99 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 91 optimal weight: 0.0000 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9069 Z= 0.182 Angle : 0.632 10.351 12320 Z= 0.310 Chirality : 0.039 0.295 1464 Planarity : 0.003 0.042 1553 Dihedral : 7.533 58.181 1458 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.02 % Allowed : 25.29 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1143 helix: 1.40 (0.19), residues: 744 sheet: -1.59 (0.77), residues: 44 loop : -2.23 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 322 HIS 0.003 0.001 HIS B 487 PHE 0.013 0.001 PHE A 190 TYR 0.015 0.001 TYR A 395 ARG 0.002 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8866 (m-30) cc_final: 0.8536 (m-30) REVERT: A 352 GLU cc_start: 0.9245 (mt-10) cc_final: 0.9037 (mp0) REVERT: A 607 MET cc_start: 0.9666 (ttt) cc_final: 0.9143 (tpt) REVERT: A 610 GLU cc_start: 0.9864 (tt0) cc_final: 0.9645 (pt0) REVERT: A 649 MET cc_start: 0.9561 (tmm) cc_final: 0.9334 (ppp) REVERT: A 653 LEU cc_start: 0.9534 (tp) cc_final: 0.9279 (mm) REVERT: B 260 CYS cc_start: 0.9444 (t) cc_final: 0.9120 (t) REVERT: B 291 MET cc_start: 0.9570 (tpt) cc_final: 0.8880 (tmm) REVERT: B 320 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8928 (mm) REVERT: B 336 MET cc_start: 0.9200 (mmt) cc_final: 0.8593 (tmm) REVERT: B 371 MET cc_start: 0.8805 (ppp) cc_final: 0.8463 (ppp) REVERT: B 465 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9240 (pp) REVERT: B 466 MET cc_start: 0.8905 (mmm) cc_final: 0.8336 (mmm) REVERT: B 548 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9367 (mm) REVERT: B 738 MET cc_start: 0.9296 (pmm) cc_final: 0.9050 (pmm) outliers start: 38 outliers final: 27 residues processed: 150 average time/residue: 0.1374 time to fit residues: 32.6593 Evaluate side-chains 149 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9069 Z= 0.285 Angle : 0.681 11.849 12320 Z= 0.345 Chirality : 0.040 0.290 1464 Planarity : 0.003 0.046 1553 Dihedral : 7.566 59.894 1458 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.19 % Allowed : 25.40 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1143 helix: 1.22 (0.19), residues: 744 sheet: -3.23 (0.97), residues: 24 loop : -2.03 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 410 HIS 0.007 0.001 HIS B 487 PHE 0.012 0.002 PHE A 221 TYR 0.014 0.002 TYR B 346 ARG 0.004 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 116 time to evaluate : 0.949 Fit side-chains REVERT: A 274 ASP cc_start: 0.8908 (m-30) cc_final: 0.8586 (m-30) REVERT: A 607 MET cc_start: 0.9671 (ttt) cc_final: 0.9289 (tpt) REVERT: A 610 GLU cc_start: 0.9867 (tt0) cc_final: 0.9653 (tp30) REVERT: A 653 LEU cc_start: 0.9561 (tp) cc_final: 0.9172 (mm) REVERT: B 260 CYS cc_start: 0.9516 (t) cc_final: 0.9196 (t) REVERT: B 320 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8964 (mm) REVERT: B 336 MET cc_start: 0.9200 (mmt) cc_final: 0.8589 (tmm) REVERT: B 466 MET cc_start: 0.8854 (mmm) cc_final: 0.8453 (mmm) REVERT: B 485 MET cc_start: 0.9055 (mmt) cc_final: 0.8305 (mmm) REVERT: B 738 MET cc_start: 0.9332 (pmm) cc_final: 0.9121 (pmm) outliers start: 49 outliers final: 39 residues processed: 148 average time/residue: 0.1409 time to fit residues: 32.8263 Evaluate side-chains 154 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9069 Z= 0.170 Angle : 0.654 12.576 12320 Z= 0.315 Chirality : 0.041 0.287 1464 Planarity : 0.003 0.044 1553 Dihedral : 7.414 57.806 1458 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.70 % Allowed : 27.30 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1143 helix: 1.46 (0.19), residues: 746 sheet: -2.54 (1.06), residues: 22 loop : -1.96 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 322 HIS 0.003 0.001 HIS A 575 PHE 0.013 0.001 PHE A 190 TYR 0.018 0.001 TYR A 598 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 0.966 Fit side-chains REVERT: A 274 ASP cc_start: 0.8904 (m-30) cc_final: 0.8574 (m-30) REVERT: A 607 MET cc_start: 0.9660 (ttt) cc_final: 0.9132 (tpt) REVERT: A 610 GLU cc_start: 0.9862 (tt0) cc_final: 0.9632 (pt0) REVERT: A 653 LEU cc_start: 0.9524 (tp) cc_final: 0.9193 (mm) REVERT: B 260 CYS cc_start: 0.9419 (t) cc_final: 0.9089 (t) REVERT: B 291 MET cc_start: 0.9548 (tpt) cc_final: 0.8819 (tmm) REVERT: B 320 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8929 (mm) REVERT: B 336 MET cc_start: 0.9205 (mmt) cc_final: 0.8598 (tmm) REVERT: B 465 LEU cc_start: 0.9563 (tt) cc_final: 0.9198 (pp) REVERT: B 466 MET cc_start: 0.8885 (mmm) cc_final: 0.8372 (mmm) REVERT: B 548 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9370 (mm) REVERT: B 738 MET cc_start: 0.9282 (pmm) cc_final: 0.9070 (pmm) outliers start: 35 outliers final: 27 residues processed: 148 average time/residue: 0.1366 time to fit residues: 31.7394 Evaluate side-chains 148 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9069 Z= 0.266 Angle : 0.695 10.910 12320 Z= 0.347 Chirality : 0.041 0.280 1464 Planarity : 0.003 0.044 1553 Dihedral : 7.409 57.996 1458 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.81 % Allowed : 27.83 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1143 helix: 1.27 (0.19), residues: 748 sheet: -2.92 (1.01), residues: 24 loop : -1.92 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 410 HIS 0.007 0.001 HIS B 487 PHE 0.012 0.002 PHE A 190 TYR 0.016 0.001 TYR A 598 ARG 0.004 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 1.130 Fit side-chains REVERT: A 274 ASP cc_start: 0.8928 (m-30) cc_final: 0.8628 (m-30) REVERT: A 607 MET cc_start: 0.9662 (ttt) cc_final: 0.9289 (tpt) REVERT: A 610 GLU cc_start: 0.9864 (tt0) cc_final: 0.9653 (tp30) REVERT: B 260 CYS cc_start: 0.9516 (t) cc_final: 0.9185 (t) REVERT: B 291 MET cc_start: 0.9539 (tpt) cc_final: 0.8834 (tmm) REVERT: B 320 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8969 (mm) REVERT: B 336 MET cc_start: 0.9204 (mmt) cc_final: 0.8598 (tmm) REVERT: B 465 LEU cc_start: 0.9600 (tt) cc_final: 0.9291 (pp) REVERT: B 466 MET cc_start: 0.8875 (mmm) cc_final: 0.8342 (mmm) REVERT: B 548 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9376 (mm) outliers start: 36 outliers final: 29 residues processed: 143 average time/residue: 0.1443 time to fit residues: 32.6772 Evaluate side-chains 146 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.0060 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9069 Z= 0.164 Angle : 0.689 12.599 12320 Z= 0.325 Chirality : 0.041 0.274 1464 Planarity : 0.003 0.049 1553 Dihedral : 7.290 57.478 1458 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.54 % Allowed : 29.10 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1143 helix: 1.55 (0.19), residues: 748 sheet: -1.93 (1.15), residues: 22 loop : -1.87 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 322 HIS 0.003 0.001 HIS A 575 PHE 0.017 0.001 PHE B 605 TYR 0.020 0.001 TYR A 598 ARG 0.002 0.000 ARG B 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8908 (m-30) cc_final: 0.8607 (m-30) REVERT: A 465 LEU cc_start: 0.9779 (tt) cc_final: 0.9569 (pp) REVERT: A 544 CYS cc_start: 0.9494 (m) cc_final: 0.9288 (m) REVERT: A 607 MET cc_start: 0.9649 (ttt) cc_final: 0.9275 (tpt) REVERT: A 610 GLU cc_start: 0.9860 (tt0) cc_final: 0.9652 (tp30) REVERT: B 260 CYS cc_start: 0.9398 (t) cc_final: 0.9043 (t) REVERT: B 291 MET cc_start: 0.9496 (tpt) cc_final: 0.8800 (tmm) REVERT: B 320 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8924 (mm) REVERT: B 336 MET cc_start: 0.9204 (mmt) cc_final: 0.8588 (tmm) REVERT: B 466 MET cc_start: 0.8863 (mmm) cc_final: 0.8451 (mmm) REVERT: B 485 MET cc_start: 0.8958 (mmt) cc_final: 0.8173 (mmm) REVERT: B 548 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9364 (mm) REVERT: B 549 GLU cc_start: 0.9181 (pt0) cc_final: 0.8971 (pt0) outliers start: 24 outliers final: 18 residues processed: 153 average time/residue: 0.1437 time to fit residues: 34.1826 Evaluate side-chains 151 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.040888 restraints weight = 49305.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.042483 restraints weight = 29026.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.043652 restraints weight = 20080.124| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9069 Z= 0.171 Angle : 0.706 11.914 12320 Z= 0.336 Chirality : 0.042 0.284 1464 Planarity : 0.003 0.051 1553 Dihedral : 7.231 57.550 1458 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.12 % Allowed : 30.16 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1143 helix: 1.49 (0.19), residues: 748 sheet: -1.71 (1.18), residues: 22 loop : -1.84 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 322 HIS 0.003 0.001 HIS A 575 PHE 0.014 0.001 PHE B 605 TYR 0.018 0.001 TYR A 346 ARG 0.007 0.000 ARG B 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.81 seconds wall clock time: 32 minutes 27.32 seconds (1947.32 seconds total)