Starting phenix.real_space_refine on Sun Nov 17 05:16:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgz_41247/11_2024/8tgz_41247_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgz_41247/11_2024/8tgz_41247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgz_41247/11_2024/8tgz_41247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgz_41247/11_2024/8tgz_41247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgz_41247/11_2024/8tgz_41247_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgz_41247/11_2024/8tgz_41247_trim.cif" } resolution = 3.78 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= -0.001 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: 5 Type Number sf(0) Gaussians S 39 5.16 5 C 4195 2.51 5 N 1125 2.21 5 O 1339 1.98 5 H 6122 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12820 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3395 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "E" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3129 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3104 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1531 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1480 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 94} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.84, per 1000 atoms: 0.53 Number of scatterers: 12820 At special positions: 0 Unit cell: (108.587, 102.637, 136.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 O 1339 8.00 N 1125 7.00 C 4195 6.00 H 6122 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 452 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 486 " distance=2.04 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 552 " distance=2.04 Simple disulfide: pdb=" SG CYS A 569 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS M 133 " - pdb=" SG CYS M 193 " distance=2.03 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 201 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA B 3 " - " BMA B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " BMA D 3 " - " BMA D 4 " BETA1-6 " BMA B 3 " - " BMA B 5 " NAG-ASN " NAG A 701 " - " ASN A 448 " " NAG A 702 " - " ASN A 532 " " NAG A 703 " - " ASN A 430 " " NAG B 1 " - " ASN A 423 " " NAG C 1 " - " ASN A 540 " " NAG D 1 " - " ASN A 556 " Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 19 sheets defined 9.9% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 437 through 442 removed outlier: 4.230A pdb=" N PHE A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 4.053A pdb=" N ARG A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.964A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'E' and resid 206 through 209 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 78 through 82 removed outlier: 4.056A pdb=" N GLU F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.658A pdb=" N SER F 126 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'M' and resid 122 through 127 Processing helix chain 'N' and resid 159 through 163 Processing helix chain 'N' and resid 190 through 196 removed outlier: 3.563A pdb=" N GLY N 195 " --> pdb=" O SER N 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR N 196 " --> pdb=" O SER N 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.597A pdb=" N VAL A 516 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 506 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 551 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 498 Processing sheet with id=AA3, first strand: chain 'A' and resid 602 through 604 removed outlier: 7.517A pdb=" N TRP A 602 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 609 " --> pdb=" O TRP A 602 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 604 " --> pdb=" O CYS A 607 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 17 through 23 Processing sheet with id=AA5, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.864A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS E 96 " --> pdb=" O TRP E 109 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP E 109 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 98 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP E 107 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.864A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 125 through 129 removed outlier: 4.128A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 125 through 129 removed outlier: 4.128A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AB1, first strand: chain 'F' and resid 9 through 12 removed outlier: 5.775A pdb=" N GLN F 36 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU F 45 " --> pdb=" O GLN F 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AB3, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'F' and resid 113 through 117 removed outlier: 6.281A pdb=" N TYR F 172 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AB6, first strand: chain 'M' and resid 114 through 117 removed outlier: 3.714A pdb=" N VAL M 132 " --> pdb=" O PHE M 117 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN M 137 " --> pdb=" O TYR M 172 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR M 172 " --> pdb=" O ASN M 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 144 through 147 removed outlier: 3.673A pdb=" N LYS M 144 " --> pdb=" O THR M 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 125 through 129 Processing sheet with id=AB9, first strand: chain 'N' and resid 125 through 129 Processing sheet with id=AC1, first strand: chain 'N' and resid 155 through 158 274 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 6118 1.05 - 1.26: 1065 1.26 - 1.47: 2881 1.47 - 1.68: 2885 1.68 - 1.89: 46 Bond restraints: 12995 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CB CYS A 552 " pdb=" SG CYS A 552 " ideal model delta sigma weight residual 1.808 1.727 0.081 3.30e-02 9.18e+02 6.07e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.357 0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" CB CYS A 508 " pdb=" SG CYS A 508 " ideal model delta sigma weight residual 1.808 1.889 -0.081 3.30e-02 9.18e+02 5.95e+00 ... (remaining 12990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 23122 2.72 - 5.44: 150 5.44 - 8.16: 19 8.16 - 10.88: 3 10.88 - 13.59: 2 Bond angle restraints: 23296 Sorted by residual: angle pdb=" CA CYS A 552 " pdb=" CB CYS A 552 " pdb=" SG CYS A 552 " ideal model delta sigma weight residual 114.40 126.37 -11.97 2.30e+00 1.89e-01 2.71e+01 angle pdb=" CG ASN A 556 " pdb=" ND2 ASN A 556 " pdb="HD21 ASN A 556 " ideal model delta sigma weight residual 120.00 106.41 13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" N CYS A 552 " pdb=" CA CYS A 552 " pdb=" C CYS A 552 " ideal model delta sigma weight residual 107.88 114.01 -6.13 1.41e+00 5.03e-01 1.89e+01 angle pdb=" CB ASN A 556 " pdb=" CG ASN A 556 " pdb=" ND2 ASN A 556 " ideal model delta sigma weight residual 116.40 122.25 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" CB LYS A 596 " pdb=" CG LYS A 596 " pdb=" CD LYS A 596 " ideal model delta sigma weight residual 111.30 118.49 -7.19 2.30e+00 1.89e-01 9.76e+00 ... (remaining 23291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 5924 24.85 - 49.70: 424 49.70 - 74.56: 117 74.56 - 99.41: 58 99.41 - 124.26: 28 Dihedral angle restraints: 6551 sinusoidal: 3578 harmonic: 2973 Sorted by residual: dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 486 " pdb=" CB CYS A 486 " ideal model delta sinusoidal sigma weight residual -86.00 -152.43 66.43 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 157.89 -64.89 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CB CYS A 452 " pdb=" SG CYS A 452 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual 93.00 149.25 -56.25 1 1.00e+01 1.00e-02 4.27e+01 ... (remaining 6548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 1086 0.198 - 0.397: 7 0.397 - 0.595: 1 0.595 - 0.794: 0 0.794 - 0.992: 2 Chirality restraints: 1096 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 556 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 430 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 540 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 1093 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 452 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO A 453 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 206 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO N 207 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO N 207 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 207 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 460 " 0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A 461 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " 0.035 5.00e-02 4.00e+02 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 530 2.16 - 2.77: 22891 2.77 - 3.38: 31861 3.38 - 3.99: 41744 3.99 - 4.60: 63350 Nonbonded interactions: 160376 Sorted by model distance: nonbonded pdb=" OE1 GLN E 62 " pdb=" H GLN E 62 " model vdw 1.546 2.450 nonbonded pdb=" OE2 GLU M 142 " pdb="HE21 GLN M 198 " model vdw 1.553 2.450 nonbonded pdb=" OD1 ASP A 520 " pdb=" H ARG A 521 " model vdw 1.567 2.450 nonbonded pdb="HE21 GLN F 6 " pdb=" O GLY F 99 " model vdw 1.581 2.450 nonbonded pdb=" OE1 GLU N 153 " pdb=" H GLU N 153 " model vdw 1.581 2.450 ... (remaining 160371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.500 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: 0.220 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.310 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.004 0.104 6873 Z= 0.301 Angle : 0.785 11.975 9394 Z= 0.376 Chirality : 0.066 0.992 1096 Planarity : 0.006 0.080 1193 Dihedral : 24.265 124.259 2612 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.14 % Allowed : 22.44 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.95 (0.28), residues: 857 helix: -1.27 (1.01), residues: 32 sheet: 0.81 (0.29), residues: 322 loop : -1.67 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 469 HIS 0.003 0.001 HIS A 421 PHE 0.012 0.001 PHE A 509 TYR 0.021 0.001 TYR N 150 ARG 0.004 0.000 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 413 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it. Evaluate side-chains 139 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.4270 time to fit residues: 76.3353 Evaluate side-chains 133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.0570 chunk 34 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6873 Z= 0.227 Angle : 0.726 12.401 9394 Z= 0.346 Chirality : 0.057 0.720 1096 Planarity : 0.006 0.063 1193 Dihedral : 21.999 115.192 1216 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.26 % Allowed : 20.90 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.98 (0.28), residues: 857 helix: -1.56 (0.94), residues: 32 sheet: 0.75 (0.30), residues: 317 loop : -1.61 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 554 HIS 0.003 0.001 HIS A 649 PHE 0.009 0.001 PHE F 97 TYR 0.012 0.001 TYR F 35 ARG 0.003 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 413 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it. Evaluate side-chains 143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.025 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 outliers start: 9 outliers final: 5 residues processed: 138 average time/residue: 0.4392 time to fit residues: 78.9683 Evaluate side-chains 134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 6873 Z= 0.252 Angle : 0.719 12.691 9394 Z= 0.338 Chirality : 0.055 0.707 1096 Planarity : 0.005 0.061 1193 Dihedral : 18.100 109.465 1216 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.17 % Favored : 91.72 % Rotamer: Outliers : 2.38 % Allowed : 20.76 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -1.00 (0.28), residues: 857 helix: -1.63 (0.92), residues: 32 sheet: 0.71 (0.29), residues: 324 loop : -1.63 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 109 HIS 0.003 0.001 HIS A 649 PHE 0.008 0.001 PHE F 97 TYR 0.016 0.001 TYR N 150 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 413 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it. Evaluate side-chains 151 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.037 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: A 454 GLU cc_start: 0.8291 (tp30) cc_final: 0.8015 (mp0) REVERT: F 93 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8492 (p) REVERT: M 149 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8101 (p) outliers start: 17 outliers final: 11 residues processed: 144 average time/residue: 0.4401 time to fit residues: 81.7676 Evaluate side-chains 143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 196 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6873 Z= 0.246 Angle : 0.685 12.767 9394 Z= 0.327 Chirality : 0.054 0.686 1096 Planarity : 0.005 0.061 1193 Dihedral : 16.831 107.577 1216 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.40 % Favored : 91.48 % Rotamer: Outliers : 2.24 % Allowed : 21.18 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -1.00 (0.28), residues: 857 helix: -1.58 (0.93), residues: 32 sheet: 0.67 (0.29), residues: 324 loop : -1.60 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 109 HIS 0.004 0.001 HIS A 649 PHE 0.009 0.001 PHE F 97 TYR 0.016 0.001 TYR N 150 ARG 0.007 0.000 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 413 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it. Evaluate side-chains 146 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.060 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: A 454 GLU cc_start: 0.8250 (tp30) cc_final: 0.7941 (mp0) REVERT: F 93 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8515 (p) REVERT: M 149 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8154 (p) REVERT: M 150 ASP cc_start: 0.8602 (t0) cc_final: 0.8385 (t0) REVERT: N 209 ASN cc_start: 0.7819 (m-40) cc_final: 0.7033 (p0) outliers start: 16 outliers final: 10 residues processed: 137 average time/residue: 0.4397 time to fit residues: 78.5649 Evaluate side-chains 138 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 196 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 6873 Z= 0.263 Angle : 0.682 12.750 9394 Z= 0.327 Chirality : 0.053 0.677 1096 Planarity : 0.005 0.060 1193 Dihedral : 16.384 106.695 1216 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.75 % Favored : 91.13 % Rotamer: Outliers : 2.38 % Allowed : 21.32 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -1.00 (0.28), residues: 857 helix: -1.61 (0.92), residues: 32 sheet: 0.70 (0.29), residues: 323 loop : -1.61 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 109 HIS 0.003 0.001 HIS M 197 PHE 0.010 0.001 PHE F 97 TYR 0.015 0.001 TYR N 150 ARG 0.001 0.000 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 413 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it. Evaluate side-chains 141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.8409 (tp30) cc_final: 0.8081 (mp0) REVERT: F 93 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8538 (p) REVERT: M 149 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8172 (p) REVERT: M 150 ASP cc_start: 0.8647 (t0) cc_final: 0.8429 (t0) REVERT: N 209 ASN cc_start: 0.7826 (m-40) cc_final: 0.7032 (p0) outliers start: 17 outliers final: 14 residues processed: 135 average time/residue: 0.4116 time to fit residues: 72.4142 Evaluate side-chains 138 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 196 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 6873 Z= 0.257 Angle : 0.682 12.864 9394 Z= 0.328 Chirality : 0.053 0.663 1096 Planarity : 0.005 0.060 1193 Dihedral : 15.793 106.142 1216 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.98 % Favored : 90.90 % Rotamer: Outliers : 3.37 % Allowed : 20.62 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -1.00 (0.28), residues: 857 helix: -1.53 (0.93), residues: 32 sheet: 0.67 (0.29), residues: 323 loop : -1.60 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 109 HIS 0.003 0.001 HIS A 638 PHE 0.010 0.001 PHE N 151 TYR 0.024 0.002 TYR N 150 ARG 0.003 0.000 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 413 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it. Evaluate side-chains 143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.8428 (tp30) cc_final: 0.8079 (mp0) REVERT: E 46 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6962 (mt-10) REVERT: M 149 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8335 (p) REVERT: M 150 ASP cc_start: 0.8645 (t0) cc_final: 0.8424 (t0) REVERT: N 209 ASN cc_start: 0.7822 (m-40) cc_final: 0.7033 (p0) outliers start: 24 outliers final: 19 residues processed: 136 average time/residue: 0.4163 time to fit residues: 73.7367 Evaluate side-chains 138 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 196 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6873 Z= 0.219 Angle : 0.671 12.916 9394 Z= 0.321 Chirality : 0.053 0.656 1096 Planarity : 0.005 0.059 1193 Dihedral : 15.549 105.879 1216 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.52 % Favored : 91.37 % Rotamer: Outliers : 2.81 % Allowed : 21.04 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.94 (0.28), residues: 857 helix: -1.47 (0.94), residues: 32 sheet: 0.74 (0.29), residues: 316 loop : -1.55 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 487 HIS 0.002 0.001 HIS A 638 PHE 0.009 0.001 PHE F 97 TYR 0.017 0.001 TYR N 150 ARG 0.002 0.000 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 413 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it. Evaluate side-chains 142 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.8422 (tp30) cc_final: 0.8183 (mp0) REVERT: F 34 TRP cc_start: 0.8930 (m100) cc_final: 0.8350 (m-90) REVERT: M 149 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8135 (p) REVERT: N 209 ASN cc_start: 0.7898 (m-40) cc_final: 0.7138 (p0) outliers start: 20 outliers final: 18 residues processed: 136 average time/residue: 0.4261 time to fit residues: 76.9079 Evaluate side-chains 139 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 196 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 74 optimal weight: 0.0870 chunk 78 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 HIS E 43 GLN M 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6873 Z= 0.226 Angle : 0.671 12.989 9394 Z= 0.320 Chirality : 0.052 0.652 1096 Planarity : 0.005 0.059 1193 Dihedral : 15.176 105.196 1216 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.52 % Favored : 91.37 % Rotamer: Outliers : 2.95 % Allowed : 21.04 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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 (0.28), residues: 857 helix: -1.41 (0.94), residues: 32 sheet: 0.75 (0.29), residues: 312 loop : -1.50 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 109 HIS 0.002 0.001 HIS A 638 PHE 0.009 0.001 PHE F 97 TYR 0.022 0.001 TYR N 150 ARG 0.002 0.000 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 413 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it. Evaluate side-chains 143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.8413 (tp30) cc_final: 0.8177 (mp0) REVERT: F 34 TRP cc_start: 0.8918 (m100) cc_final: 0.8357 (m-90) REVERT: M 149 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8135 (p) outliers start: 21 outliers final: 19 residues processed: 136 average time/residue: 0.4073 time to fit residues: 72.7611 Evaluate side-chains 142 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 196 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6873 Z= 0.240 Angle : 0.676 12.974 9394 Z= 0.323 Chirality : 0.052 0.641 1096 Planarity : 0.005 0.059 1193 Dihedral : 14.850 104.397 1216 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.87 % Favored : 91.02 % Rotamer: Outliers : 3.09 % Allowed : 21.04 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.86 (0.28), residues: 857 helix: -0.92 (1.02), residues: 26 sheet: 0.75 (0.29), residues: 310 loop : -1.47 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 469 HIS 0.003 0.001 HIS A 649 PHE 0.009 0.001 PHE F 97 TYR 0.025 0.001 TYR N 150 ARG 0.003 0.000 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 413 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it. Evaluate side-chains 143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.8411 (tp30) cc_final: 0.8176 (mp0) REVERT: F 34 TRP cc_start: 0.8894 (m100) cc_final: 0.8292 (m-90) REVERT: M 149 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8125 (p) outliers start: 22 outliers final: 20 residues processed: 135 average time/residue: 0.3959 time to fit residues: 70.1510 Evaluate side-chains 139 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 196 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.0020 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 overall best weight: 0.3766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6873 Z= 0.200 Angle : 0.661 13.010 9394 Z= 0.316 Chirality : 0.051 0.628 1096 Planarity : 0.005 0.059 1193 Dihedral : 14.559 104.313 1216 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.93 % Favored : 91.95 % Rotamer: Outliers : 2.10 % Allowed : 22.30 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.77 (0.29), residues: 857 helix: -0.89 (1.03), residues: 27 sheet: 0.80 (0.29), residues: 312 loop : -1.41 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 159 HIS 0.002 0.000 HIS A 649 PHE 0.010 0.001 PHE A 509 TYR 0.020 0.001 TYR N 150 ARG 0.002 0.000 ARG F 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 413 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it. Evaluate side-chains 133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.8372 (tp30) cc_final: 0.8155 (mp0) REVERT: F 34 TRP cc_start: 0.8783 (m100) cc_final: 0.8174 (m-90) REVERT: M 149 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8026 (p) outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.4180 time to fit residues: 71.1031 Evaluate side-chains 128 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 196 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 69 optimal weight: 0.4980 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.1980 chunk 59 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.163414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132721 restraints weight = 31246.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138252 restraints weight = 16944.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141899 restraints weight = 11429.597| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 6873 Z= 0.192 Angle : 0.661 13.045 9394 Z= 0.314 Chirality : 0.051 0.620 1096 Planarity : 0.005 0.058 1193 Dihedral : 14.289 103.488 1216 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.28 % Favored : 91.60 % Rotamer: Outliers : 1.82 % Allowed : 23.14 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.71 (0.29), residues: 857 helix: -0.83 (1.04), residues: 27 sheet: 0.85 (0.29), residues: 312 loop : -1.37 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 469 HIS 0.002 0.000 HIS A 649 PHE 0.009 0.001 PHE A 509 TYR 0.023 0.001 TYR N 150 ARG 0.002 0.000 ARG F 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3468.46 seconds wall clock time: 62 minutes 39.12 seconds (3759.12 seconds total)