Starting phenix.real_space_refine on Thu Jul 31 01:10:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgz_41247/07_2025/8tgz_41247_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgz_41247/07_2025/8tgz_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/cci-nas-00/data/ceres_data/8tgz_41247/07_2025/8tgz_41247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgz_41247/07_2025/8tgz_41247.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgz_41247/07_2025/8tgz_41247_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgz_41247/07_2025/8tgz_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.93, per 1000 atoms: 0.54 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: 1.36 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: 4.35 Time building geometry restraints manager: 4.23 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: 1.520 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: 0.250 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.870 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.320 ------------------------------------------------------------------------------- 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 6901 Z= 0.203 Angle : 0.978 24.722 9464 Z= 0.424 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01991 ( 6) link_NAG-ASN : angle 10.51128 ( 18) link_BETA1-4 : bond 0.02635 ( 6) link_BETA1-4 : angle 7.93821 ( 18) hydrogen bonds : bond 0.12382 ( 226) hydrogen bonds : angle 6.39144 ( 669) link_BETA1-6 : bond 0.00294 ( 1) link_BETA1-6 : angle 2.50983 ( 3) SS BOND : bond 0.00503 ( 14) SS BOND : angle 2.08204 ( 28) link_BETA1-3 : bond 0.00274 ( 1) link_BETA1-3 : angle 1.23582 ( 3) covalent geometry : bond 0.00437 ( 6873) covalent geometry : angle 0.78484 ( 9394) *********************** 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 : 0.945 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: 0.4069 time to fit residues: 73.2920 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 : 1.048 ------------------------------------------------------------------------------- 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: 0.8980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.163584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132781 restraints weight = 30997.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138418 restraints weight = 16424.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142156 restraints weight = 10997.929| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.004 0.082 6901 Z= 0.147 Angle : 0.811 18.937 9464 Z= 0.367 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01385 ( 6) link_NAG-ASN : angle 6.62426 ( 18) link_BETA1-4 : bond 0.01213 ( 6) link_BETA1-4 : angle 4.33032 ( 18) hydrogen bonds : bond 0.03767 ( 226) hydrogen bonds : angle 5.82584 ( 669) link_BETA1-6 : bond 0.00366 ( 1) link_BETA1-6 : angle 3.01783 ( 3) SS BOND : bond 0.00450 ( 14) SS BOND : angle 1.87487 ( 28) link_BETA1-3 : bond 0.00081 ( 1) link_BETA1-3 : angle 2.52030 ( 3) covalent geometry : bond 0.00346 ( 6873) covalent geometry : angle 0.72555 ( 9394) *********************** 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 : 1.051 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: 0.4222 time to fit residues: 75.2777 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 : 0.984 ------------------------------------------------------------------------------- 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 13 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 0.0050 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.164240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133541 restraints weight = 30888.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139209 restraints weight = 16567.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142861 restraints weight = 11103.736| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6901 Z= 0.139 Angle : 0.790 15.250 9464 Z= 0.353 Chirality : 0.055 0.708 1096 Planarity : 0.005 0.061 1193 Dihedral : 18.287 109.720 1216 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.10 % Allowed : 20.48 % 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: -0.93 (0.28), residues: 857 helix: -1.59 (0.93), residues: 32 sheet: 0.78 (0.30), residues: 317 loop : -1.56 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 109 HIS 0.003 0.001 HIS A 649 PHE 0.008 0.001 PHE N 151 TYR 0.015 0.001 TYR N 150 ARG 0.001 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.01484 ( 6) link_NAG-ASN : angle 6.45865 ( 18) link_BETA1-4 : bond 0.01063 ( 6) link_BETA1-4 : angle 3.99721 ( 18) hydrogen bonds : bond 0.03551 ( 226) hydrogen bonds : angle 5.61537 ( 669) link_BETA1-6 : bond 0.00104 ( 1) link_BETA1-6 : angle 2.13218 ( 3) SS BOND : bond 0.00441 ( 14) SS BOND : angle 1.79403 ( 28) link_BETA1-3 : bond 0.00053 ( 1) link_BETA1-3 : angle 2.99623 ( 3) covalent geometry : bond 0.00334 ( 6873) covalent geometry : angle 0.70994 ( 9394) *********************** 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 154 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.006 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: 0.8261 (tp30) cc_final: 0.7978 (mp0) REVERT: M 149 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7971 (p) outliers start: 15 outliers final: 10 residues processed: 148 average time/residue: 0.4373 time to fit residues: 82.9499 Evaluate side-chains 145 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 66 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 4 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.163501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132779 restraints weight = 30938.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138406 restraints weight = 16664.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142103 restraints weight = 11186.633| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6901 Z= 0.140 Angle : 0.741 13.696 9464 Z= 0.339 Chirality : 0.054 0.687 1096 Planarity : 0.005 0.060 1193 Dihedral : 16.866 107.429 1216 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.28 % Favored : 91.60 % Rotamer: Outliers : 1.96 % Allowed : 20.76 % Favored : 77.28 % 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: -0.91 (0.28), residues: 857 helix: -1.69 (0.90), residues: 33 sheet: 0.77 (0.29), residues: 317 loop : -1.53 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 109 HIS 0.003 0.001 HIS A 649 PHE 0.009 0.001 PHE F 97 TYR 0.014 0.001 TYR N 150 ARG 0.007 0.000 ARG A 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00968 ( 6) link_NAG-ASN : angle 5.40959 ( 18) link_BETA1-4 : bond 0.00903 ( 6) link_BETA1-4 : angle 3.67469 ( 18) hydrogen bonds : bond 0.03346 ( 226) hydrogen bonds : angle 5.50884 ( 669) link_BETA1-6 : bond 0.00345 ( 1) link_BETA1-6 : angle 1.91618 ( 3) SS BOND : bond 0.00444 ( 14) SS BOND : angle 1.80471 ( 28) link_BETA1-3 : bond 0.00058 ( 1) link_BETA1-3 : angle 3.21810 ( 3) covalent geometry : bond 0.00343 ( 6873) covalent geometry : angle 0.67638 ( 9394) *********************** 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 147 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.091 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: symmetry clash REVERT: A 454 GLU cc_start: 0.8200 (tp30) cc_final: 0.7916 (mp0) REVERT: M 149 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8124 (p) REVERT: M 150 ASP cc_start: 0.8501 (t0) cc_final: 0.8288 (t0) outliers start: 14 outliers final: 10 residues processed: 140 average time/residue: 0.4372 time to fit residues: 80.5392 Evaluate side-chains 141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 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 500 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 166 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 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.0570 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.162617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131861 restraints weight = 30764.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137448 restraints weight = 16583.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141106 restraints weight = 11154.353| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6901 Z= 0.145 Angle : 0.732 12.798 9464 Z= 0.336 Chirality : 0.053 0.672 1096 Planarity : 0.005 0.057 1193 Dihedral : 16.178 106.135 1216 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.28 % Favored : 91.60 % Rotamer: Outliers : 2.52 % Allowed : 20.76 % Favored : 76.72 % 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: -0.88 (0.28), residues: 857 helix: -1.54 (0.93), residues: 32 sheet: 0.76 (0.29), residues: 323 loop : -1.52 (0.26), residues: 502 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 0.023 0.001 TYR N 150 ARG 0.002 0.000 ARG F 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00895 ( 6) link_NAG-ASN : angle 5.04762 ( 18) link_BETA1-4 : bond 0.00879 ( 6) link_BETA1-4 : angle 3.69399 ( 18) hydrogen bonds : bond 0.03355 ( 226) hydrogen bonds : angle 5.46439 ( 669) link_BETA1-6 : bond 0.00337 ( 1) link_BETA1-6 : angle 1.79417 ( 3) SS BOND : bond 0.00436 ( 14) SS BOND : angle 1.82569 ( 28) link_BETA1-3 : bond 0.00077 ( 1) link_BETA1-3 : angle 3.28627 ( 3) covalent geometry : bond 0.00356 ( 6873) covalent geometry : angle 0.67122 ( 9394) *********************** 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 151 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.996 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: 0.8359 (tp30) cc_final: 0.8053 (mp0) REVERT: M 149 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8154 (p) REVERT: M 150 ASP cc_start: 0.8566 (t0) cc_final: 0.8355 (t0) outliers start: 18 outliers final: 16 residues processed: 142 average time/residue: 0.4095 time to fit residues: 75.7711 Evaluate side-chains 144 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 557 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 E residue 185 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 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 ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.161389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130319 restraints weight = 31471.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135901 restraints weight = 17045.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139549 restraints weight = 11512.004| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 6901 Z= 0.161 Angle : 0.734 12.883 9464 Z= 0.338 Chirality : 0.053 0.664 1096 Planarity : 0.005 0.057 1193 Dihedral : 15.680 105.795 1216 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.98 % Favored : 90.90 % Rotamer: Outliers : 3.09 % Allowed : 21.32 % 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: -0.93 (0.28), residues: 857 helix: -1.55 (0.92), residues: 32 sheet: 0.74 (0.29), residues: 324 loop : -1.58 (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 M 197 PHE 0.010 0.001 PHE F 97 TYR 0.020 0.001 TYR N 150 ARG 0.003 0.000 ARG A 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 6) link_NAG-ASN : angle 4.76326 ( 18) link_BETA1-4 : bond 0.00841 ( 6) link_BETA1-4 : angle 3.64404 ( 18) hydrogen bonds : bond 0.03397 ( 226) hydrogen bonds : angle 5.48973 ( 669) link_BETA1-6 : bond 0.00333 ( 1) link_BETA1-6 : angle 1.76220 ( 3) SS BOND : bond 0.00438 ( 14) SS BOND : angle 1.85906 ( 28) link_BETA1-3 : bond 0.00131 ( 1) link_BETA1-3 : angle 3.32962 ( 3) covalent geometry : bond 0.00394 ( 6873) covalent geometry : angle 0.67727 ( 9394) *********************** 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 148 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.990 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: 0.8381 (tp30) cc_final: 0.8068 (mp0) REVERT: E 60 TYR cc_start: 0.7854 (m-80) cc_final: 0.7380 (m-80) REVERT: M 149 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8221 (p) REVERT: M 150 ASP cc_start: 0.8568 (t0) cc_final: 0.8351 (t0) REVERT: N 209 ASN cc_start: 0.7837 (m-40) cc_final: 0.7026 (p0) outliers start: 22 outliers final: 17 residues processed: 137 average time/residue: 0.3921 time to fit residues: 71.0130 Evaluate side-chains 145 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 557 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 166 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 80 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.161089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130116 restraints weight = 31162.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135655 restraints weight = 16930.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139270 restraints weight = 11464.974| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6901 Z= 0.155 Angle : 0.728 12.864 9464 Z= 0.336 Chirality : 0.053 0.656 1096 Planarity : 0.005 0.058 1193 Dihedral : 15.373 105.308 1216 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.98 % Favored : 90.90 % Rotamer: Outliers : 2.95 % Allowed : 20.62 % Favored : 76.44 % 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: -1.56 (0.91), residues: 33 sheet: 0.74 (0.29), residues: 324 loop : -1.58 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 487 HIS 0.003 0.001 HIS M 197 PHE 0.010 0.001 PHE F 97 TYR 0.020 0.001 TYR N 150 ARG 0.002 0.000 ARG E 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 6) link_NAG-ASN : angle 4.61842 ( 18) link_BETA1-4 : bond 0.00867 ( 6) link_BETA1-4 : angle 3.64820 ( 18) hydrogen bonds : bond 0.03355 ( 226) hydrogen bonds : angle 5.46079 ( 669) link_BETA1-6 : bond 0.00349 ( 1) link_BETA1-6 : angle 1.77053 ( 3) SS BOND : bond 0.00427 ( 14) SS BOND : angle 1.81851 ( 28) link_BETA1-3 : bond 0.00096 ( 1) link_BETA1-3 : angle 3.38586 ( 3) covalent geometry : bond 0.00379 ( 6873) covalent geometry : angle 0.67314 ( 9394) *********************** 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 149 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.8387 (tp30) cc_final: 0.8174 (mp0) REVERT: E 60 TYR cc_start: 0.7875 (m-80) cc_final: 0.7382 (m-80) REVERT: F 34 TRP cc_start: 0.8937 (m100) cc_final: 0.8379 (m-90) REVERT: M 149 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8324 (p) REVERT: N 209 ASN cc_start: 0.7827 (m-40) cc_final: 0.7031 (p0) outliers start: 21 outliers final: 18 residues processed: 139 average time/residue: 0.4703 time to fit residues: 88.4468 Evaluate side-chains 146 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 557 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 627 PHE 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 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 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 0.0870 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.161681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130705 restraints weight = 31483.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136306 restraints weight = 17001.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139953 restraints weight = 11436.710| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6901 Z= 0.134 Angle : 0.723 12.961 9464 Z= 0.333 Chirality : 0.052 0.643 1096 Planarity : 0.005 0.057 1193 Dihedral : 15.099 105.058 1216 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.75 % Favored : 91.13 % Rotamer: Outliers : 2.52 % Allowed : 21.32 % 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: -0.84 (0.28), residues: 857 helix: -1.48 (0.92), residues: 33 sheet: 0.83 (0.29), residues: 312 loop : -1.48 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.003 0.000 ARG F 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00804 ( 6) link_NAG-ASN : angle 4.47246 ( 18) link_BETA1-4 : bond 0.00896 ( 6) link_BETA1-4 : angle 3.60646 ( 18) hydrogen bonds : bond 0.03219 ( 226) hydrogen bonds : angle 5.37308 ( 669) link_BETA1-6 : bond 0.00389 ( 1) link_BETA1-6 : angle 1.76923 ( 3) SS BOND : bond 0.00499 ( 14) SS BOND : angle 2.06979 ( 28) link_BETA1-3 : bond 0.00059 ( 1) link_BETA1-3 : angle 3.44337 ( 3) covalent geometry : bond 0.00333 ( 6873) covalent geometry : angle 0.66773 ( 9394) *********************** 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 147 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.992 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: 0.8380 (tp30) cc_final: 0.8101 (mp0) REVERT: E 60 TYR cc_start: 0.7859 (m-80) cc_final: 0.7376 (m-80) REVERT: F 34 TRP cc_start: 0.8905 (m100) cc_final: 0.8332 (m-90) REVERT: M 149 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8155 (p) outliers start: 18 outliers final: 17 residues processed: 139 average time/residue: 0.3901 time to fit residues: 71.6605 Evaluate side-chains 144 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 A residue 627 PHE 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 91 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 60 optimal weight: 0.0870 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.162243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.131323 restraints weight = 31271.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136853 restraints weight = 16953.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140552 restraints weight = 11437.469| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6901 Z= 0.127 Angle : 0.713 13.021 9464 Z= 0.329 Chirality : 0.052 0.633 1096 Planarity : 0.005 0.058 1193 Dihedral : 14.758 104.446 1216 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.75 % Favored : 91.13 % Rotamer: Outliers : 2.10 % Allowed : 22.16 % Favored : 75.74 % 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: -0.73 (0.29), residues: 857 helix: -0.86 (1.03), residues: 27 sheet: 0.85 (0.29), residues: 312 loop : -1.40 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 487 HIS 0.003 0.001 HIS N 205 PHE 0.009 0.001 PHE F 97 TYR 0.023 0.001 TYR N 150 ARG 0.003 0.000 ARG F 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 6) link_NAG-ASN : angle 4.37191 ( 18) link_BETA1-4 : bond 0.00901 ( 6) link_BETA1-4 : angle 3.57951 ( 18) hydrogen bonds : bond 0.03099 ( 226) hydrogen bonds : angle 5.29763 ( 669) link_BETA1-6 : bond 0.00365 ( 1) link_BETA1-6 : angle 1.74383 ( 3) SS BOND : bond 0.00463 ( 14) SS BOND : angle 1.99573 ( 28) link_BETA1-3 : bond 0.00040 ( 1) link_BETA1-3 : angle 3.47102 ( 3) covalent geometry : bond 0.00316 ( 6873) covalent geometry : angle 0.65905 ( 9394) *********************** 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 141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 TYR cc_start: 0.7861 (m-80) cc_final: 0.7279 (m-80) REVERT: F 34 TRP cc_start: 0.8825 (m100) cc_final: 0.8279 (m-90) REVERT: M 149 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8082 (p) REVERT: M 150 ASP cc_start: 0.8564 (t0) cc_final: 0.8352 (t0) outliers start: 15 outliers final: 14 residues processed: 134 average time/residue: 0.3900 time to fit residues: 68.6672 Evaluate side-chains 138 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 548 ASN Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 627 PHE 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 F residue 160 GLU Chi-restraints excluded: chain F residue 173 SER 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 46 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN M 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129759 restraints weight = 31291.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135282 restraints weight = 17040.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138925 restraints weight = 11528.406| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6901 Z= 0.159 Angle : 0.726 13.001 9464 Z= 0.336 Chirality : 0.052 0.638 1096 Planarity : 0.005 0.057 1193 Dihedral : 14.500 103.243 1216 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.10 % Favored : 90.78 % Rotamer: Outliers : 2.66 % Allowed : 22.02 % Favored : 75.32 % 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: -0.81 (0.28), residues: 857 helix: -1.02 (0.99), residues: 27 sheet: 0.83 (0.29), residues: 310 loop : -1.47 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 109 HIS 0.003 0.001 HIS M 197 PHE 0.010 0.001 PHE F 97 TYR 0.022 0.001 TYR N 150 ARG 0.002 0.000 ARG F 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00772 ( 6) link_NAG-ASN : angle 4.36700 ( 18) link_BETA1-4 : bond 0.00897 ( 6) link_BETA1-4 : angle 3.63353 ( 18) hydrogen bonds : bond 0.03301 ( 226) hydrogen bonds : angle 5.35848 ( 669) link_BETA1-6 : bond 0.00309 ( 1) link_BETA1-6 : angle 1.77535 ( 3) SS BOND : bond 0.00472 ( 14) SS BOND : angle 1.95790 ( 28) link_BETA1-3 : bond 0.00055 ( 1) link_BETA1-3 : angle 3.42754 ( 3) covalent geometry : bond 0.00392 ( 6873) covalent geometry : angle 0.67357 ( 9394) ********************** 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 141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 TYR cc_start: 0.7680 (m-80) cc_final: 0.7097 (m-80) REVERT: F 34 TRP cc_start: 0.8917 (m100) cc_final: 0.8385 (m-90) REVERT: M 149 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8157 (p) REVERT: M 150 ASP cc_start: 0.8616 (t0) cc_final: 0.8392 (t0) outliers start: 19 outliers final: 18 residues processed: 134 average time/residue: 0.3941 time to fit residues: 70.2405 Evaluate side-chains 142 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 A residue 627 PHE 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 91 ASP 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 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 65 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 55 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.161779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130755 restraints weight = 31214.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136256 restraints weight = 17039.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139884 restraints weight = 11539.545| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6901 Z= 0.132 Angle : 0.716 13.009 9464 Z= 0.330 Chirality : 0.051 0.623 1096 Planarity : 0.005 0.058 1193 Dihedral : 14.290 103.154 1216 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.05 % Favored : 91.83 % Rotamer: Outliers : 2.38 % Allowed : 22.02 % 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 (0.28), residues: 857 helix: -0.91 (1.01), residues: 27 sheet: 0.85 (0.29), residues: 310 loop : -1.44 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 487 HIS 0.002 0.001 HIS A 649 PHE 0.009 0.001 PHE F 97 TYR 0.021 0.001 TYR N 150 ARG 0.003 0.000 ARG F 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00771 ( 6) link_NAG-ASN : angle 4.27929 ( 18) link_BETA1-4 : bond 0.00932 ( 6) link_BETA1-4 : angle 3.69942 ( 18) hydrogen bonds : bond 0.03137 ( 226) hydrogen bonds : angle 5.29256 ( 669) link_BETA1-6 : bond 0.00377 ( 1) link_BETA1-6 : angle 1.78460 ( 3) SS BOND : bond 0.00466 ( 14) SS BOND : angle 2.02750 ( 28) link_BETA1-3 : bond 0.00056 ( 1) link_BETA1-3 : angle 3.50073 ( 3) covalent geometry : bond 0.00327 ( 6873) covalent geometry : angle 0.66170 ( 9394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4728.51 seconds wall clock time: 82 minutes 35.11 seconds (4955.11 seconds total)