Starting phenix.real_space_refine on Sat Dec 28 03:07:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9coo_45787/12_2024/9coo_45787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9coo_45787/12_2024/9coo_45787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9coo_45787/12_2024/9coo_45787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9coo_45787/12_2024/9coo_45787.map" model { file = "/net/cci-nas-00/data/ceres_data/9coo_45787/12_2024/9coo_45787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9coo_45787/12_2024/9coo_45787.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Ca 3 9.91 5 S 36 5.16 5 C 4685 2.51 5 N 1266 2.21 5 O 1503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7493 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3170 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 11, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 155 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 926 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 923 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 769 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 859 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 801 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 91 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 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.45, per 1000 atoms: 0.73 Number of scatterers: 7493 At special positions: 0 Unit cell: (104.58, 117.86, 126.16, 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) Ca 3 19.99 S 36 16.00 O 1503 8.00 N 1266 7.00 C 4685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 68 " - pdb=" SG CYS R 82 " distance=2.03 Simple disulfide: pdb=" SG CYS R 75 " - pdb=" SG CYS R 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 121 " distance=2.04 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 143 " distance=2.03 Simple disulfide: pdb=" SG CYS R 148 " - pdb=" SG CYS R 160 " distance=2.03 Simple disulfide: pdb=" SG CYS R 155 " - pdb=" SG CYS R 173 " distance=2.03 Simple disulfide: pdb=" SG CYS R 167 " - pdb=" SG CYS R 184 " distance=2.03 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 NAG-ASN " NAG A4601 " - " ASN A3336 " " NAG A4602 " - " ASN A3101 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.0 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 11 sheets defined 13.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 335 through 353 removed outlier: 4.163A pdb=" N ALA B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 removed outlier: 3.783A pdb=" N ALA B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.612A pdb=" N GLU B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 removed outlier: 4.077A pdb=" N SER B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 428 " --> pdb=" O PHE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 448 Processing helix chain 'B' and resid 451 through 469 Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.937A pdb=" N LEU L 89 " --> pdb=" O PRO L 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.756A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'R' and resid 137 through 142 removed outlier: 3.855A pdb=" N SER R 142 " --> pdb=" O SER R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 2825 through 2831 removed outlier: 3.570A pdb=" N VAL A2828 " --> pdb=" O HIS A2839 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS A2839 " --> pdb=" O VAL A2828 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A2846 " --> pdb=" O ALA A2849 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A2849 " --> pdb=" O PHE A2846 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A2858 " --> pdb=" O LEU A2869 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR A2866 " --> pdb=" O LYS A2892 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A2868 " --> pdb=" O PHE A2890 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A2890 " --> pdb=" O GLU A2868 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A2906 " --> pdb=" O TYR A2889 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A2895 " --> pdb=" O PHE A2900 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2918 through 2922 current: chain 'A' and resid 2939 through 2951 removed outlier: 3.649A pdb=" N ASN A2961 " --> pdb=" O GLN A2972 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2968 through 2975 current: chain 'A' and resid 3000 through 3009 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3015 through 3023 current: chain 'A' and resid 3030 through 3031 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3030 through 3031 current: chain 'A' and resid 3064 through 3074 removed outlier: 4.172A pdb=" N ASP A3069 " --> pdb=" O ARG A3092 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A3092 " --> pdb=" O ASP A3069 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A3090 " --> pdb=" O LEU A3071 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A3098 " --> pdb=" O ALA A3091 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A3096 " --> pdb=" O PHE A3093 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3337 through 3344 removed outlier: 3.669A pdb=" N ALA A3364 " --> pdb=" O THR A3385 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A3385 " --> pdb=" O ALA A3364 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A3366 " --> pdb=" O GLY A3383 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY A3383 " --> pdb=" O LEU A3366 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 46 through 51 removed outlier: 4.836A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'L' and resid 39 through 44 removed outlier: 6.306A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 59 through 60 current: chain 'L' and resid 102 through 103 Processing sheet with id=AA7, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.549A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.434A pdb=" N GLY N 10 " --> pdb=" O THR N 120 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N SER N 122 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL N 12 " --> pdb=" O SER N 122 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 72 through 74 Processing sheet with id=AB1, first strand: chain 'R' and resid 113 through 115 Processing sheet with id=AB2, first strand: chain 'R' and resid 152 through 154 removed outlier: 3.590A pdb=" N ILE R 161 " --> pdb=" O PHE R 153 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2471 1.34 - 1.46: 1309 1.46 - 1.57: 3811 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 7638 Sorted by residual: bond pdb=" CB ASP L 66 " pdb=" CG ASP L 66 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.30e+00 bond pdb=" CB ASN B 379 " pdb=" CG ASN B 379 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CB GLU A2826 " pdb=" CG GLU A2826 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.73e-01 bond pdb=" CB CYS H 96 " pdb=" SG CYS H 96 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 9.73e-01 bond pdb=" CA ASN H 77 " pdb=" CB ASN H 77 " ideal model delta sigma weight residual 1.527 1.543 -0.015 1.61e-02 3.86e+03 9.17e-01 ... (remaining 7633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 10183 1.92 - 3.84: 185 3.84 - 5.75: 25 5.75 - 7.67: 11 7.67 - 9.59: 4 Bond angle restraints: 10408 Sorted by residual: angle pdb=" CA ARG B 345 " pdb=" CB ARG B 345 " pdb=" CG ARG B 345 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" C2 NAG A4602 " pdb=" N2 NAG A4602 " pdb=" C7 NAG A4602 " ideal model delta sigma weight residual 124.56 133.57 -9.01 3.00e+00 1.11e-01 9.03e+00 angle pdb=" CB ARG B 345 " pdb=" CG ARG B 345 " pdb=" CD ARG B 345 " ideal model delta sigma weight residual 111.30 118.00 -6.70 2.30e+00 1.89e-01 8.49e+00 angle pdb=" CA LEU A2869 " pdb=" CB LEU A2869 " pdb=" CG LEU A2869 " ideal model delta sigma weight residual 116.30 125.89 -9.59 3.50e+00 8.16e-02 7.51e+00 angle pdb=" CB MET A3007 " pdb=" CG MET A3007 " pdb=" SD MET A3007 " ideal model delta sigma weight residual 112.70 120.87 -8.17 3.00e+00 1.11e-01 7.41e+00 ... (remaining 10403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 3870 16.47 - 32.93: 485 32.93 - 49.40: 145 49.40 - 65.87: 41 65.87 - 82.34: 5 Dihedral angle restraints: 4546 sinusoidal: 1606 harmonic: 2940 Sorted by residual: dihedral pdb=" CB CYS R 155 " pdb=" SG CYS R 155 " pdb=" SG CYS R 173 " pdb=" CB CYS R 173 " ideal model delta sinusoidal sigma weight residual -86.00 -143.19 57.19 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CB CYS R 109 " pdb=" SG CYS R 109 " pdb=" SG CYS R 121 " pdb=" CB CYS R 121 " ideal model delta sinusoidal sigma weight residual -86.00 -142.47 56.47 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" CB CYS R 68 " pdb=" SG CYS R 68 " pdb=" SG CYS R 82 " pdb=" CB CYS R 82 " ideal model delta sinusoidal sigma weight residual 93.00 146.80 -53.80 1 1.00e+01 1.00e-02 3.93e+01 ... (remaining 4543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1017 0.056 - 0.112: 160 0.112 - 0.168: 25 0.168 - 0.224: 0 0.224 - 0.279: 2 Chirality restraints: 1204 Sorted by residual: chirality pdb=" C1 NAG A4602 " pdb=" ND2 ASN A3101 " pdb=" C2 NAG A4602 " pdb=" O5 NAG A4602 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CG LEU B 462 " pdb=" CB LEU B 462 " pdb=" CD1 LEU B 462 " pdb=" CD2 LEU B 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C2 NAG A4602 " pdb=" C1 NAG A4602 " pdb=" C3 NAG A4602 " pdb=" N2 NAG A4602 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1201 not shown) Planarity restraints: 1359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A2971 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ASN A2971 " 0.055 2.00e-02 2.50e+03 pdb=" O ASN A2971 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A2972 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 83 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO R 84 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 84 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 84 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A2895 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A2896 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A2896 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A2896 " 0.021 5.00e-02 4.00e+02 ... (remaining 1356 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 577 2.73 - 3.27: 8002 3.27 - 3.81: 12364 3.81 - 4.36: 14118 4.36 - 4.90: 24213 Nonbonded interactions: 59274 Sorted by model distance: nonbonded pdb=" OD2 ASP B 448 " pdb=" ND2 ASN B 454 " model vdw 2.182 3.120 nonbonded pdb=" OD1 ASP R 170 " pdb="CA CA R 903 " model vdw 2.226 2.510 nonbonded pdb=" OE2 GLU R 101 " pdb="CA CA R 901 " model vdw 2.233 2.510 nonbonded pdb=" O SER R 130 " pdb=" OG SER R 130 " model vdw 2.235 3.040 nonbonded pdb=" O TYR A3379 " pdb=" NZ LYS A3380 " model vdw 2.236 3.120 ... (remaining 59269 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.640 Find NCS groups from input model: 0.120 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 : 0.003 0.043 7638 Z= 0.226 Angle : 0.663 9.589 10408 Z= 0.334 Chirality : 0.043 0.279 1204 Planarity : 0.004 0.051 1357 Dihedral : 16.582 82.337 2620 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.45 % Allowed : 32.36 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.26), residues: 1006 helix: -0.50 (0.46), residues: 123 sheet: -1.96 (0.24), residues: 441 loop : -1.69 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 87 HIS 0.011 0.001 HIS N 104 PHE 0.015 0.001 PHE A3038 TYR 0.016 0.001 TYR B 342 ARG 0.003 0.000 ARG A2836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.7825 (tmm) cc_final: 0.6856 (tmm) REVERT: A 3174 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7628 (mtpt) REVERT: A 3340 ASP cc_start: 0.7895 (p0) cc_final: 0.7523 (m-30) REVERT: B 456 LEU cc_start: 0.8882 (tp) cc_final: 0.8604 (tt) REVERT: H 29 PHE cc_start: 0.8251 (t80) cc_final: 0.7677 (t80) REVERT: H 108 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: L 79 LEU cc_start: 0.7855 (tp) cc_final: 0.7254 (pp) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.1777 time to fit residues: 27.2396 Evaluate side-chains 106 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7638 Z= 0.269 Angle : 0.645 9.661 10408 Z= 0.329 Chirality : 0.044 0.328 1204 Planarity : 0.004 0.048 1357 Dihedral : 5.752 53.560 1146 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.23 % Allowed : 28.93 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.26), residues: 1006 helix: 0.38 (0.49), residues: 121 sheet: -1.91 (0.25), residues: 425 loop : -1.69 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 165 HIS 0.010 0.001 HIS N 104 PHE 0.017 0.002 PHE B 424 TYR 0.016 0.002 TYR A3177 ARG 0.003 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.889 Fit side-chains REVERT: A 2843 MET cc_start: 0.7730 (tmm) cc_final: 0.6885 (tmm) REVERT: A 2933 CYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6387 (m) REVERT: A 3106 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7005 (m-40) REVERT: A 3126 LEU cc_start: 0.7779 (tp) cc_final: 0.7540 (tp) REVERT: A 3174 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7595 (mtpt) REVERT: A 3340 ASP cc_start: 0.7743 (p0) cc_final: 0.7332 (m-30) REVERT: B 456 LEU cc_start: 0.8914 (tp) cc_final: 0.8445 (tt) REVERT: H 108 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: R 168 ASP cc_start: 0.8325 (m-30) cc_final: 0.7767 (p0) outliers start: 32 outliers final: 16 residues processed: 124 average time/residue: 0.1727 time to fit residues: 30.2037 Evaluate side-chains 110 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3021 HIS Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7638 Z= 0.281 Angle : 0.645 9.439 10408 Z= 0.327 Chirality : 0.044 0.312 1204 Planarity : 0.004 0.049 1357 Dihedral : 5.879 54.584 1146 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 5.94 % Allowed : 27.21 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.27), residues: 1006 helix: 0.60 (0.50), residues: 121 sheet: -1.99 (0.25), residues: 424 loop : -1.65 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 165 HIS 0.010 0.001 HIS N 104 PHE 0.016 0.002 PHE B 424 TYR 0.015 0.002 TYR A3177 ARG 0.003 0.001 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.7957 (tmm) cc_final: 0.7083 (tmm) REVERT: A 2933 CYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6340 (m) REVERT: A 3097 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8425 (tptm) REVERT: A 3166 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8238 (tptp) REVERT: A 3174 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7562 (mtpt) REVERT: A 3340 ASP cc_start: 0.7992 (p0) cc_final: 0.7600 (m-30) REVERT: B 341 TRP cc_start: 0.7818 (m100) cc_final: 0.7599 (m100) REVERT: B 360 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6215 (tt0) REVERT: B 456 LEU cc_start: 0.8962 (tp) cc_final: 0.8720 (mt) REVERT: B 464 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: H 76 LYS cc_start: 0.8219 (pttm) cc_final: 0.8013 (pttp) REVERT: H 108 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7239 (m-80) REVERT: N 45 ARG cc_start: 0.7515 (ttp-110) cc_final: 0.7192 (ttp-110) outliers start: 45 outliers final: 28 residues processed: 135 average time/residue: 0.1875 time to fit residues: 35.1935 Evaluate side-chains 128 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3097 LYS Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3353 ASN Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 381 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2839 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7638 Z= 0.269 Angle : 0.654 13.898 10408 Z= 0.327 Chirality : 0.043 0.302 1204 Planarity : 0.004 0.048 1357 Dihedral : 5.868 54.664 1145 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 6.34 % Allowed : 26.82 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.26), residues: 1006 helix: 0.58 (0.51), residues: 121 sheet: -1.95 (0.25), residues: 422 loop : -1.65 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.009 0.001 HIS N 104 PHE 0.015 0.002 PHE B 424 TYR 0.019 0.002 TYR A2889 ARG 0.005 0.001 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2843 MET cc_start: 0.7952 (tmm) cc_final: 0.7177 (tmm) REVERT: A 2844 LEU cc_start: 0.7515 (mm) cc_final: 0.7245 (mp) REVERT: A 2933 CYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6308 (m) REVERT: A 3097 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8429 (tptm) REVERT: A 3126 LEU cc_start: 0.7858 (tp) cc_final: 0.7534 (tp) REVERT: A 3166 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8198 (tptp) REVERT: A 3174 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7534 (mtpt) REVERT: A 3359 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.4650 (pm20) REVERT: B 360 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6249 (tt0) REVERT: B 456 LEU cc_start: 0.8971 (tp) cc_final: 0.8737 (mt) REVERT: B 464 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: H 108 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7158 (m-80) outliers start: 48 outliers final: 35 residues processed: 138 average time/residue: 0.1922 time to fit residues: 36.3627 Evaluate side-chains 135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2898 LEU Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3021 HIS Chi-restraints excluded: chain A residue 3097 LYS Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3353 ASN Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3359 GLN Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 381 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 0.0030 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7638 Z= 0.235 Angle : 0.627 10.036 10408 Z= 0.315 Chirality : 0.043 0.294 1204 Planarity : 0.004 0.049 1357 Dihedral : 5.825 54.760 1145 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 6.47 % Allowed : 27.61 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.26), residues: 1006 helix: 0.71 (0.53), residues: 116 sheet: -1.88 (0.25), residues: 421 loop : -1.60 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.009 0.001 HIS N 104 PHE 0.010 0.001 PHE B 424 TYR 0.021 0.002 TYR B 342 ARG 0.004 0.001 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 97 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 2822 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7006 (mm) REVERT: A 2843 MET cc_start: 0.8028 (tmm) cc_final: 0.7159 (tmm) REVERT: A 2844 LEU cc_start: 0.7498 (mm) cc_final: 0.7254 (mp) REVERT: A 2933 CYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6250 (m) REVERT: A 3097 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8404 (tptm) REVERT: A 3126 LEU cc_start: 0.7888 (tp) cc_final: 0.7686 (tp) REVERT: A 3166 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8164 (tptp) REVERT: A 3174 LYS cc_start: 0.7746 (mmtm) cc_final: 0.7449 (mtpt) REVERT: A 3359 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.4634 (pm20) REVERT: B 360 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.6261 (tt0) REVERT: B 403 ASN cc_start: 0.8663 (t0) cc_final: 0.8437 (t0) REVERT: B 456 LEU cc_start: 0.8967 (tp) cc_final: 0.8736 (mt) REVERT: B 464 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: H 108 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7177 (m-80) outliers start: 49 outliers final: 34 residues processed: 135 average time/residue: 0.1907 time to fit residues: 35.0625 Evaluate side-chains 132 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 90 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2898 LEU Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3097 LYS Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3353 ASN Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3359 GLN Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 381 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 7638 Z= 0.386 Angle : 0.727 9.549 10408 Z= 0.370 Chirality : 0.045 0.301 1204 Planarity : 0.005 0.051 1357 Dihedral : 6.354 54.999 1145 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 8.19 % Allowed : 26.68 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.26), residues: 1006 helix: 0.44 (0.51), residues: 117 sheet: -2.13 (0.24), residues: 443 loop : -1.65 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 113 HIS 0.010 0.001 HIS N 104 PHE 0.015 0.002 PHE A3038 TYR 0.019 0.002 TYR L 92 ARG 0.005 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 94 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8017 (tmm) cc_final: 0.7129 (tmm) REVERT: A 2933 CYS cc_start: 0.6638 (OUTLIER) cc_final: 0.5998 (m) REVERT: A 3097 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8454 (tppt) REVERT: A 3126 LEU cc_start: 0.8028 (tp) cc_final: 0.7753 (tp) REVERT: A 3166 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8212 (tptp) REVERT: A 3359 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.4681 (pm20) REVERT: B 360 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.6310 (tt0) REVERT: B 426 GLU cc_start: 0.7051 (pp20) cc_final: 0.6797 (pp20) REVERT: B 464 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: H 29 PHE cc_start: 0.8284 (t80) cc_final: 0.7746 (t80) REVERT: H 76 LYS cc_start: 0.8045 (pttp) cc_final: 0.7843 (pttp) REVERT: H 79 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8315 (tp) REVERT: H 108 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7206 (m-80) outliers start: 62 outliers final: 44 residues processed: 143 average time/residue: 0.1917 time to fit residues: 37.6119 Evaluate side-chains 138 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 86 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2829 LYS Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2891 HIS Chi-restraints excluded: chain A residue 2928 SER Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2944 SER Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3077 PHE Chi-restraints excluded: chain A residue 3097 LYS Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3353 ASN Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3359 GLN Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 381 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 97 TYR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.0170 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 0.0770 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7638 Z= 0.191 Angle : 0.627 9.855 10408 Z= 0.313 Chirality : 0.043 0.285 1204 Planarity : 0.004 0.049 1357 Dihedral : 5.866 58.900 1145 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.15 % Allowed : 29.99 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.27), residues: 1006 helix: 0.82 (0.52), residues: 121 sheet: -1.91 (0.25), residues: 423 loop : -1.50 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.009 0.001 HIS N 104 PHE 0.019 0.001 PHE B 340 TYR 0.024 0.001 TYR B 342 ARG 0.002 0.000 ARG A2836 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2822 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.6971 (mm) REVERT: A 2843 MET cc_start: 0.8031 (tmm) cc_final: 0.7191 (tmm) REVERT: A 2844 LEU cc_start: 0.7457 (mm) cc_final: 0.7198 (mp) REVERT: A 2933 CYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6967 (m) REVERT: A 3126 LEU cc_start: 0.7978 (tp) cc_final: 0.7698 (tp) REVERT: A 3166 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.8020 (tptp) REVERT: B 341 TRP cc_start: 0.7636 (m100) cc_final: 0.7342 (m100) REVERT: B 360 GLN cc_start: 0.6732 (OUTLIER) cc_final: 0.6291 (tt0) REVERT: B 456 LEU cc_start: 0.8958 (tp) cc_final: 0.8755 (mt) REVERT: H 79 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8221 (tp) REVERT: H 108 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: N 5 GLN cc_start: 0.4161 (OUTLIER) cc_final: 0.3745 (pm20) REVERT: N 38 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8054 (ttp-170) outliers start: 39 outliers final: 22 residues processed: 135 average time/residue: 0.1852 time to fit residues: 34.8016 Evaluate side-chains 122 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2928 SER Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3384 THR Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2848 ASN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 7638 Z= 0.464 Angle : 0.773 9.600 10408 Z= 0.398 Chirality : 0.046 0.297 1204 Planarity : 0.005 0.053 1357 Dihedral : 6.408 55.213 1144 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 7.66 % Allowed : 28.40 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.27), residues: 1006 helix: 0.30 (0.51), residues: 115 sheet: -2.16 (0.24), residues: 438 loop : -1.68 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 113 HIS 0.011 0.002 HIS N 104 PHE 0.016 0.002 PHE A3038 TYR 0.023 0.003 TYR L 92 ARG 0.004 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 88 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8005 (tmm) cc_final: 0.7194 (tmm) REVERT: A 2933 CYS cc_start: 0.6439 (OUTLIER) cc_final: 0.5297 (m) REVERT: A 3166 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8204 (tptp) REVERT: A 3359 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.4713 (pm20) REVERT: B 360 GLN cc_start: 0.6758 (OUTLIER) cc_final: 0.6398 (tt0) REVERT: B 464 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: H 29 PHE cc_start: 0.8288 (t80) cc_final: 0.7732 (t80) REVERT: H 79 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8322 (tp) REVERT: H 108 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7216 (m-80) outliers start: 58 outliers final: 42 residues processed: 135 average time/residue: 0.1743 time to fit residues: 32.8709 Evaluate side-chains 133 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 84 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2891 HIS Chi-restraints excluded: chain A residue 2928 SER Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2944 SER Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3077 PHE Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3353 ASN Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3359 GLN Chi-restraints excluded: chain A residue 3384 THR Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 97 TYR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 114 PHE Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 ASP Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 94 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3094 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7638 Z= 0.259 Angle : 0.684 10.163 10408 Z= 0.345 Chirality : 0.043 0.296 1204 Planarity : 0.004 0.051 1357 Dihedral : 5.931 54.511 1144 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.15 % Allowed : 30.78 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.27), residues: 1006 helix: 0.64 (0.51), residues: 121 sheet: -2.06 (0.25), residues: 432 loop : -1.60 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.009 0.001 HIS N 104 PHE 0.016 0.002 PHE N 68 TYR 0.021 0.002 TYR A2889 ARG 0.002 0.000 ARG A2836 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8051 (tmm) cc_final: 0.7294 (tmm) REVERT: A 2933 CYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7053 (m) REVERT: A 3166 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8045 (tptp) REVERT: B 360 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6368 (tt0) REVERT: B 464 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: H 29 PHE cc_start: 0.8261 (t80) cc_final: 0.7728 (t80) REVERT: H 79 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8234 (tp) REVERT: H 108 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6992 (m-80) outliers start: 39 outliers final: 31 residues processed: 129 average time/residue: 0.1891 time to fit residues: 34.1767 Evaluate side-chains 131 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2891 HIS Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3384 THR Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 114 PHE Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 84 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7638 Z= 0.212 Angle : 0.671 10.662 10408 Z= 0.335 Chirality : 0.043 0.283 1204 Planarity : 0.004 0.052 1357 Dihedral : 5.637 54.695 1144 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.62 % Allowed : 31.70 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.27), residues: 1006 helix: 0.86 (0.52), residues: 121 sheet: -1.92 (0.25), residues: 416 loop : -1.55 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.009 0.001 HIS N 104 PHE 0.018 0.001 PHE A3038 TYR 0.023 0.001 TYR A2889 ARG 0.004 0.001 ARG A2836 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8011 (tmm) cc_final: 0.7249 (tmm) REVERT: A 2844 LEU cc_start: 0.7505 (mm) cc_final: 0.7267 (mp) REVERT: A 2933 CYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7061 (m) REVERT: A 3166 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8056 (tptp) REVERT: B 360 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6363 (tt0) REVERT: B 464 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: H 29 PHE cc_start: 0.8250 (t80) cc_final: 0.7732 (t80) REVERT: H 79 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8178 (tp) REVERT: H 108 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.7026 (m-80) REVERT: N 5 GLN cc_start: 0.4759 (OUTLIER) cc_final: 0.4302 (pm20) REVERT: N 38 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8089 (ttp-170) outliers start: 35 outliers final: 27 residues processed: 131 average time/residue: 0.1868 time to fit residues: 33.7090 Evaluate side-chains 133 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3077 PHE Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3384 THR Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 114 PHE Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.0000 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 overall best weight: 0.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.113019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.099688 restraints weight = 23252.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.101305 restraints weight = 13685.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.102360 restraints weight = 9621.045| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7638 Z= 0.214 Angle : 0.672 11.003 10408 Z= 0.337 Chirality : 0.042 0.260 1204 Planarity : 0.004 0.050 1357 Dihedral : 5.545 55.126 1144 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.42 % Allowed : 30.91 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.27), residues: 1006 helix: 1.22 (0.53), residues: 116 sheet: -1.79 (0.25), residues: 418 loop : -1.38 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 87 HIS 0.011 0.001 HIS A3114 PHE 0.018 0.001 PHE B 340 TYR 0.023 0.001 TYR A2889 ARG 0.007 0.001 ARG A3389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1806.15 seconds wall clock time: 33 minutes 48.02 seconds (2028.02 seconds total)