Starting phenix.real_space_refine on Wed Feb 14 05:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/02_2024/8bpg_16152.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/02_2024/8bpg_16152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/02_2024/8bpg_16152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/02_2024/8bpg_16152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/02_2024/8bpg_16152.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/02_2024/8bpg_16152.pdb" } resolution = 3.1 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= 0.008 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 46 5.16 5 C 5444 2.51 5 N 1468 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 423": "NH1" <-> "NH2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 451": "NH1" <-> "NH2" Residue "D ARG 461": "NH1" <-> "NH2" Residue "D ARG 467": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 423": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C ARG 546": "NH1" <-> "NH2" Residue "C TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "E ARG 423": "NH1" <-> "NH2" Residue "E ARG 443": "NH1" <-> "NH2" Residue "E ARG 451": "NH1" <-> "NH2" Residue "E ARG 461": "NH1" <-> "NH2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "E ARG 491": "NH1" <-> "NH2" Residue "E TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ARG 423": "NH1" <-> "NH2" Residue "F ARG 443": "NH1" <-> "NH2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 514": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8650 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "C" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "A" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.37, per 1000 atoms: 0.62 Number of scatterers: 8650 At special positions: 0 Unit cell: (117.72, 124.2, 102.6, 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 46 16.00 O 1692 8.00 N 1468 7.00 C 5444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.05 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS C 414 " distance=2.17 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.05 Simple disulfide: pdb=" SG CYS E 414 " - pdb=" SG CYS F 414 " distance=2.10 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C 601 " - " ASN C 563 " " NAG F 601 " - " ASN F 563 " " NAG G 1 " - " ASN D 563 " " NAG H 1 " - " ASN E 563 " Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 26 sheets defined 11.9% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.815A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 466 removed outlier: 3.765A pdb=" N ASN D 465 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 466 " --> pdb=" O GLN D 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 462 through 466' Processing helix chain 'D' and resid 496 through 498 No H-bonds generated for 'chain 'D' and resid 496 through 498' Processing helix chain 'D' and resid 524 through 530 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.604A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 525 through 530 Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.815A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 466 removed outlier: 3.764A pdb=" N ASN E 465 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 466 " --> pdb=" O GLN E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 466' Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 524 through 530 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 420 removed outlier: 3.603A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 466 Processing helix chain 'F' and resid 525 through 530 Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS B 37 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 86 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR B 81 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AA3, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.552A pdb=" N ARG D 346 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 380 through 384 removed outlier: 3.528A pdb=" N CYS D 426 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 439 " --> pdb=" O CYS D 426 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 428 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 399 through 400 removed outlier: 3.756A pdb=" N THR D 404 " --> pdb=" O HIS D 400 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AA9, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.767A pdb=" N ARG C 346 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 366 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.866A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 441 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 485 through 489 removed outlier: 3.604A pdb=" N THR C 535 " --> pdb=" O MET C 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS A 37 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU A 86 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 81 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AB7, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.552A pdb=" N ARG E 346 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 380 through 384 removed outlier: 3.528A pdb=" N CYS E 426 " --> pdb=" O GLN E 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 439 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 428 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 399 through 400 removed outlier: 3.756A pdb=" N THR E 404 " --> pdb=" O HIS E 400 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AC4, first strand: chain 'F' and resid 346 through 350 removed outlier: 3.767A pdb=" N ARG F 346 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 379 through 383 removed outlier: 3.865A pdb=" N THR F 379 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE F 424 " --> pdb=" O ILE F 441 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 441 " --> pdb=" O PHE F 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 485 through 489 removed outlier: 3.606A pdb=" N THR F 535 " --> pdb=" O MET F 489 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 786 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: 2.27 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2096 1.33 - 1.45: 1768 1.45 - 1.58: 4924 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 8852 Sorted by residual: bond pdb=" N VAL C 547 " pdb=" CA VAL C 547 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.14e-02 7.69e+03 1.34e+01 bond pdb=" N VAL F 547 " pdb=" CA VAL F 547 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.29e+01 bond pdb=" N VAL F 523 " pdb=" CA VAL F 523 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.15e-02 7.56e+03 1.07e+01 bond pdb=" N VAL A 62 " pdb=" CA VAL A 62 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.07e+01 bond pdb=" N VAL C 523 " pdb=" CA VAL C 523 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.15e-02 7.56e+03 1.05e+01 ... (remaining 8847 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.32: 449 107.32 - 114.15: 5188 114.15 - 120.98: 3787 120.98 - 127.81: 2596 127.81 - 134.64: 70 Bond angle restraints: 12090 Sorted by residual: angle pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" O GLY B 107 " ideal model delta sigma weight residual 122.29 118.24 4.05 8.10e-01 1.52e+00 2.49e+01 angle pdb=" CA GLY A 107 " pdb=" C GLY A 107 " pdb=" O GLY A 107 " ideal model delta sigma weight residual 122.29 118.25 4.04 8.10e-01 1.52e+00 2.49e+01 angle pdb=" N LEU E 466 " pdb=" CA LEU E 466 " pdb=" C LEU E 466 " ideal model delta sigma weight residual 113.18 108.06 5.12 1.21e+00 6.83e-01 1.79e+01 angle pdb=" N LEU D 466 " pdb=" CA LEU D 466 " pdb=" C LEU D 466 " ideal model delta sigma weight residual 113.18 108.08 5.10 1.21e+00 6.83e-01 1.78e+01 angle pdb=" N ASN F 545 " pdb=" CA ASN F 545 " pdb=" C ASN F 545 " ideal model delta sigma weight residual 112.92 108.09 4.83 1.23e+00 6.61e-01 1.54e+01 ... (remaining 12085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 4920 16.02 - 32.04: 402 32.04 - 48.06: 114 48.06 - 64.08: 28 64.08 - 80.10: 4 Dihedral angle restraints: 5468 sinusoidal: 2240 harmonic: 3228 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 58 " pdb=" CB CYS A 58 " ideal model delta sinusoidal sigma weight residual -86.00 -143.47 57.47 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS B 49 " pdb=" SG CYS B 49 " pdb=" SG CYS B 58 " pdb=" CB CYS B 58 " ideal model delta sinusoidal sigma weight residual -86.00 -143.45 57.45 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CA CYS F 414 " pdb=" C CYS F 414 " pdb=" N GLU F 415 " pdb=" CA GLU F 415 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1394 0.165 - 0.331: 44 0.331 - 0.496: 0 0.496 - 0.661: 0 0.661 - 0.827: 2 Chirality restraints: 1440 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 563 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.39e+01 ... (remaining 1437 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 514 " -0.207 9.50e-02 1.11e+02 9.26e-02 5.28e+00 pdb=" NE ARG C 514 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 514 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 514 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 514 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 514 " 0.206 9.50e-02 1.11e+02 9.24e-02 5.24e+00 pdb=" NE ARG F 514 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 514 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 514 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 514 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 50 " 0.187 9.50e-02 1.11e+02 8.39e-02 4.34e+00 pdb=" NE ARG A 50 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 50 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 50 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 50 " 0.006 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3320 2.89 - 3.39: 7484 3.39 - 3.90: 13571 3.90 - 4.40: 14476 4.40 - 4.90: 25320 Nonbonded interactions: 64171 Sorted by model distance: nonbonded pdb=" O SER F 381 " pdb=" OG1 THR F 427 " model vdw 2.391 2.440 nonbonded pdb=" O SER C 381 " pdb=" OG1 THR C 427 " model vdw 2.391 2.440 nonbonded pdb=" OG1 THR C 383 " pdb=" O GLU C 388 " model vdw 2.401 2.440 nonbonded pdb=" OG1 THR F 383 " pdb=" O GLU F 388 " model vdw 2.401 2.440 nonbonded pdb=" OG SER C 353 " pdb=" OG SER C 356 " model vdw 2.432 2.440 ... (remaining 64166 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 345 through 568) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 345 through 568) } ncs_group { reference = chain 'G' selection = chain 'H' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.240 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: 13.390 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.550 Find NCS groups from input model: 0.520 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 0.010 0.052 8852 Z= 0.639 Angle : 1.108 6.099 12090 Z= 0.803 Chirality : 0.079 0.827 1440 Planarity : 0.008 0.093 1538 Dihedral : 12.890 80.095 3330 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.90 (0.25), residues: 1094 helix: -1.03 (0.46), residues: 114 sheet: 0.86 (0.25), residues: 436 loop : -1.80 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 528 HIS 0.006 0.001 HIS A 43 PHE 0.016 0.002 PHE D 516 TYR 0.012 0.001 TYR E 500 ARG 0.003 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.6979 (p) cc_final: 0.6749 (p) REVERT: C 463 GLN cc_start: 0.6731 (tt0) cc_final: 0.6483 (tt0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2980 time to fit residues: 88.9367 Evaluate side-chains 144 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0040 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 0.0470 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 465 ASN D 510 GLN D 529 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN A 43 HIS E 465 ASN E 510 GLN E 529 ASN ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8852 Z= 0.220 Angle : 0.657 7.117 12090 Z= 0.339 Chirality : 0.046 0.205 1440 Planarity : 0.004 0.030 1538 Dihedral : 4.830 32.817 1312 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.04 % Allowed : 10.71 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.43 (0.25), residues: 1094 helix: -0.68 (0.46), residues: 112 sheet: 1.29 (0.25), residues: 426 loop : -1.56 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 528 HIS 0.006 0.002 HIS C 400 PHE 0.011 0.001 PHE A 67 TYR 0.020 0.001 TYR E 375 ARG 0.007 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.7073 (p) cc_final: 0.6812 (p) outliers start: 20 outliers final: 14 residues processed: 166 average time/residue: 0.3294 time to fit residues: 72.9215 Evaluate side-chains 147 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 523 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 540 HIS ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8852 Z= 0.300 Angle : 0.667 8.511 12090 Z= 0.342 Chirality : 0.047 0.191 1440 Planarity : 0.004 0.056 1538 Dihedral : 4.593 25.189 1312 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.39 % Allowed : 13.27 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1094 helix: -0.56 (0.46), residues: 112 sheet: 1.02 (0.24), residues: 420 loop : -1.55 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 488 HIS 0.009 0.002 HIS D 430 PHE 0.019 0.002 PHE D 479 TYR 0.015 0.002 TYR E 500 ARG 0.007 0.001 ARG D 423 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 135 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.7013 (p) cc_final: 0.6766 (p) REVERT: E 413 ILE cc_start: 0.7314 (pt) cc_final: 0.7038 (pt) outliers start: 43 outliers final: 27 residues processed: 160 average time/residue: 0.2467 time to fit residues: 51.8458 Evaluate side-chains 151 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 523 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8852 Z= 0.248 Angle : 0.637 8.314 12090 Z= 0.327 Chirality : 0.046 0.183 1440 Planarity : 0.004 0.045 1538 Dihedral : 4.395 27.110 1312 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.18 % Allowed : 15.51 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.47 (0.25), residues: 1094 helix: -0.16 (0.50), residues: 98 sheet: 1.04 (0.24), residues: 418 loop : -1.45 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 488 HIS 0.005 0.001 HIS D 430 PHE 0.013 0.001 PHE D 479 TYR 0.019 0.001 TYR E 375 ARG 0.005 0.001 ARG F 423 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.6939 (p) cc_final: 0.6693 (p) REVERT: E 413 ILE cc_start: 0.7351 (pt) cc_final: 0.7137 (pt) outliers start: 41 outliers final: 30 residues processed: 155 average time/residue: 0.2505 time to fit residues: 50.9511 Evaluate side-chains 152 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 523 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.0570 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 400 HIS ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8852 Z= 0.223 Angle : 0.634 9.199 12090 Z= 0.324 Chirality : 0.046 0.181 1440 Planarity : 0.004 0.046 1538 Dihedral : 4.249 28.378 1312 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.59 % Allowed : 15.82 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.50 (0.25), residues: 1094 helix: -0.18 (0.51), residues: 98 sheet: 1.01 (0.24), residues: 418 loop : -1.46 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 528 HIS 0.007 0.001 HIS D 400 PHE 0.011 0.001 PHE D 479 TYR 0.020 0.001 TYR D 375 ARG 0.008 0.001 ARG D 423 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 566 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7395 (pp) outliers start: 45 outliers final: 29 residues processed: 156 average time/residue: 0.2398 time to fit residues: 49.5926 Evaluate side-chains 151 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 400 HIS ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8852 Z= 0.221 Angle : 0.645 8.455 12090 Z= 0.327 Chirality : 0.046 0.177 1440 Planarity : 0.004 0.044 1538 Dihedral : 4.215 27.858 1312 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 4.18 % Allowed : 17.45 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.51 (0.25), residues: 1094 helix: -0.18 (0.51), residues: 100 sheet: 0.92 (0.24), residues: 422 loop : -1.40 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 488 HIS 0.010 0.001 HIS D 400 PHE 0.034 0.002 PHE F 405 TYR 0.016 0.001 TYR E 375 ARG 0.007 0.000 ARG C 461 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 566 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7426 (pp) outliers start: 41 outliers final: 29 residues processed: 152 average time/residue: 0.2483 time to fit residues: 49.8490 Evaluate side-chains 151 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 104 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 0.2980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 400 HIS ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8852 Z= 0.176 Angle : 0.632 8.417 12090 Z= 0.322 Chirality : 0.045 0.178 1440 Planarity : 0.004 0.045 1538 Dihedral : 4.109 26.745 1312 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 2.86 % Allowed : 19.69 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.44 (0.25), residues: 1094 helix: -0.29 (0.49), residues: 102 sheet: 0.95 (0.24), residues: 426 loop : -1.33 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 528 HIS 0.009 0.001 HIS D 400 PHE 0.008 0.001 PHE D 479 TYR 0.015 0.001 TYR D 375 ARG 0.007 0.000 ARG C 461 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 566 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7390 (pp) outliers start: 28 outliers final: 21 residues processed: 146 average time/residue: 0.2406 time to fit residues: 46.7080 Evaluate side-chains 146 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS D 400 HIS C 439 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8852 Z= 0.216 Angle : 0.660 8.107 12090 Z= 0.335 Chirality : 0.046 0.171 1440 Planarity : 0.004 0.046 1538 Dihedral : 4.157 26.994 1312 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.12 % Favored : 94.79 % Rotamer: Outliers : 3.37 % Allowed : 20.10 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.38 (0.25), residues: 1094 helix: -0.22 (0.50), residues: 102 sheet: 1.02 (0.25), residues: 412 loop : -1.25 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 488 HIS 0.009 0.001 HIS D 400 PHE 0.016 0.001 PHE C 405 TYR 0.014 0.001 TYR C 515 ARG 0.008 0.000 ARG C 461 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 566 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7434 (pp) outliers start: 33 outliers final: 26 residues processed: 147 average time/residue: 0.2669 time to fit residues: 51.5134 Evaluate side-chains 145 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0020 chunk 97 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 0.2980 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS D 400 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8852 Z= 0.176 Angle : 0.671 9.566 12090 Z= 0.337 Chirality : 0.046 0.173 1440 Planarity : 0.004 0.038 1538 Dihedral : 4.094 26.359 1312 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 3.16 % Allowed : 19.69 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.31 (0.25), residues: 1094 helix: -0.17 (0.50), residues: 102 sheet: 1.11 (0.25), residues: 414 loop : -1.26 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 382 HIS 0.009 0.001 HIS A 43 PHE 0.040 0.001 PHE C 405 TYR 0.013 0.001 TYR C 515 ARG 0.010 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 566 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7407 (pp) outliers start: 31 outliers final: 24 residues processed: 144 average time/residue: 0.2777 time to fit residues: 52.6822 Evaluate side-chains 143 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 400 HIS D 510 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8852 Z= 0.215 Angle : 0.689 10.080 12090 Z= 0.344 Chirality : 0.047 0.230 1440 Planarity : 0.005 0.051 1538 Dihedral : 4.197 25.578 1312 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 2.76 % Allowed : 20.20 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.44 (0.25), residues: 1094 helix: -0.25 (0.49), residues: 102 sheet: 0.95 (0.24), residues: 428 loop : -1.34 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 488 HIS 0.005 0.001 HIS E 393 PHE 0.053 0.002 PHE C 405 TYR 0.013 0.001 TYR C 515 ARG 0.011 0.001 ARG A 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: F 566 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7390 (pp) outliers start: 27 outliers final: 24 residues processed: 138 average time/residue: 0.2526 time to fit residues: 46.0963 Evaluate side-chains 138 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 0.0060 chunk 79 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 HIS ** F 439 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 = 0.3874 r_free = 0.3874 target = 0.087977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.060978 restraints weight = 27264.559| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.34 r_work: 0.3086 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8852 Z= 0.180 Angle : 0.697 12.039 12090 Z= 0.344 Chirality : 0.046 0.182 1440 Planarity : 0.004 0.047 1538 Dihedral : 4.186 25.843 1312 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 2.96 % Allowed : 19.90 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.39 (0.25), residues: 1094 helix: -0.21 (0.50), residues: 102 sheet: 0.99 (0.25), residues: 428 loop : -1.32 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 382 HIS 0.004 0.001 HIS E 393 PHE 0.043 0.001 PHE C 405 TYR 0.013 0.001 TYR C 515 ARG 0.012 0.001 ARG A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2511.06 seconds wall clock time: 46 minutes 2.24 seconds (2762.24 seconds total)