Starting phenix.real_space_refine on Wed Feb 12 07:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9coo_45787/02_2025/9coo_45787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9coo_45787/02_2025/9coo_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_45787/02_2025/9coo_45787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9coo_45787/02_2025/9coo_45787.map" model { file = "/net/cci-nas-00/data/ceres_data/9coo_45787/02_2025/9coo_45787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9coo_45787/02_2025/9coo_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-5592/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: 5.90, per 1000 atoms: 0.79 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 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: 0.80 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: 2.18 Time building geometry restraints manager: 2.25 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: 3.170 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.980 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- 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 : 0.849 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: 0.1832 time to fit residues: 28.0185 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 : 0.987 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.112878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.099194 restraints weight = 22934.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.100825 restraints weight = 13701.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.101837 restraints weight = 9716.280| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 : 0.769 Fit side-chains REVERT: A 2843 MET cc_start: 0.7757 (tmm) cc_final: 0.7044 (tmm) REVERT: A 2933 CYS cc_start: 0.6541 (OUTLIER) cc_final: 0.6086 (m) REVERT: A 3106 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.7804 (m-40) REVERT: A 3126 LEU cc_start: 0.7726 (tp) cc_final: 0.7491 (tp) REVERT: A 3174 LYS cc_start: 0.7706 (mmtm) cc_final: 0.7445 (mtpt) REVERT: B 456 LEU cc_start: 0.8624 (tp) cc_final: 0.8220 (tt) REVERT: H 108 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6951 (m-80) REVERT: R 168 ASP cc_start: 0.7892 (m-30) cc_final: 0.7166 (p0) outliers start: 32 outliers final: 16 residues processed: 124 average time/residue: 0.1683 time to fit residues: 29.3917 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 : 0.845 ------------------------------------------------------------------------------- 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 79 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.110661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.097193 restraints weight = 23594.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.098686 restraints weight = 14615.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.099694 restraints weight = 10542.844| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7638 Z= 0.360 Angle : 0.697 9.546 10408 Z= 0.356 Chirality : 0.045 0.319 1204 Planarity : 0.005 0.050 1357 Dihedral : 6.153 54.467 1146 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 7.00 % Allowed : 26.42 % Favored : 66.58 % 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: -2.49 (0.26), residues: 1006 helix: 0.48 (0.51), residues: 116 sheet: -1.99 (0.25), residues: 428 loop : -1.73 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 165 HIS 0.010 0.001 HIS N 104 PHE 0.016 0.002 PHE B 424 TYR 0.016 0.002 TYR A3177 ARG 0.007 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 149 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 96 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.7974 (tmm) cc_final: 0.7314 (tmm) REVERT: A 2933 CYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5701 (m) REVERT: A 3126 LEU cc_start: 0.7888 (tp) cc_final: 0.7674 (tp) REVERT: A 3166 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8315 (tptp) REVERT: A 3359 GLN cc_start: 0.6576 (OUTLIER) cc_final: 0.4584 (pm20) REVERT: B 360 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6532 (tt0) REVERT: B 426 GLU cc_start: 0.6931 (pp20) cc_final: 0.6672 (pp20) REVERT: B 463 ASN cc_start: 0.8044 (m-40) cc_final: 0.7836 (m110) REVERT: B 464 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: H 76 LYS cc_start: 0.7677 (pttm) cc_final: 0.7467 (pttp) REVERT: H 108 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6871 (m-80) REVERT: N 45 ARG cc_start: 0.7531 (ttp-110) cc_final: 0.7234 (ttp-110) REVERT: R 168 ASP cc_start: 0.7697 (m-30) cc_final: 0.7170 (p0) outliers start: 53 outliers final: 31 residues processed: 138 average time/residue: 0.1815 time to fit residues: 34.2410 Evaluate side-chains 125 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 3021 HIS 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 3367 LEU 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 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 L residue 93 TYR Chi-restraints excluded: chain L residue 97 TYR 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 R residue 79 VAL 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 16 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 65 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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** 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 = 0.112831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.099329 restraints weight = 23208.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.100902 restraints weight = 13952.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.101896 restraints weight = 9879.456| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7638 Z= 0.227 Angle : 0.639 13.559 10408 Z= 0.317 Chirality : 0.043 0.291 1204 Planarity : 0.004 0.049 1357 Dihedral : 5.827 54.241 1145 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.55 % Allowed : 27.48 % Favored : 66.97 % 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: -2.29 (0.27), residues: 1006 helix: 0.66 (0.52), residues: 121 sheet: -1.88 (0.25), residues: 415 loop : -1.63 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 165 HIS 0.010 0.001 HIS N 104 PHE 0.014 0.001 PHE A3038 TYR 0.021 0.002 TYR A2889 ARG 0.004 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 144 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 2822 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7125 (mm) REVERT: A 2843 MET cc_start: 0.8080 (tmm) cc_final: 0.7512 (tmm) REVERT: A 2844 LEU cc_start: 0.7277 (mm) cc_final: 0.6992 (mp) REVERT: A 2933 CYS cc_start: 0.6471 (OUTLIER) cc_final: 0.6058 (m) REVERT: A 3126 LEU cc_start: 0.7871 (tp) cc_final: 0.7639 (tp) REVERT: B 360 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: B 456 LEU cc_start: 0.8665 (tp) cc_final: 0.8437 (mt) REVERT: B 464 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: H 108 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: N 65 LYS cc_start: 0.8598 (tppt) cc_final: 0.8314 (tppt) outliers start: 42 outliers final: 28 residues processed: 135 average time/residue: 0.1845 time to fit residues: 34.6356 Evaluate side-chains 123 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 3164 THR 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 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 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 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 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 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 82 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 88 optimal weight: 0.0170 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- 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 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 = 0.4093 r_free = 0.4093 target = 0.113917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.100489 restraints weight = 23022.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.102093 restraints weight = 13791.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.103099 restraints weight = 9703.440| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7638 Z= 0.190 Angle : 0.619 10.348 10408 Z= 0.309 Chirality : 0.043 0.287 1204 Planarity : 0.004 0.049 1357 Dihedral : 5.711 54.407 1145 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.02 % Allowed : 28.80 % 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: -2.20 (0.27), residues: 1006 helix: 0.79 (0.54), residues: 116 sheet: -1.81 (0.25), residues: 421 loop : -1.57 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 165 HIS 0.009 0.001 HIS N 104 PHE 0.010 0.001 PHE B 424 TYR 0.017 0.001 TYR A3177 ARG 0.003 0.000 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 135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8066 (tmm) cc_final: 0.7508 (tmm) REVERT: A 2844 LEU cc_start: 0.7260 (mm) cc_final: 0.6996 (mp) REVERT: A 2933 CYS cc_start: 0.6444 (OUTLIER) cc_final: 0.6044 (m) REVERT: B 360 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6479 (tt0) REVERT: B 464 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: H 108 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6755 (m-80) outliers start: 38 outliers final: 27 residues processed: 128 average time/residue: 0.1785 time to fit residues: 31.7900 Evaluate side-chains 120 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 3106 ASN Chi-restraints excluded: chain A residue 3164 THR 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 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 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 18 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.110744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.098421 restraints weight = 23273.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.098572 restraints weight = 16305.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.098905 restraints weight = 14277.115| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1929 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= 0.370 Angle : 0.716 10.560 10408 Z= 0.363 Chirality : 0.045 0.295 1204 Planarity : 0.005 0.052 1357 Dihedral : 6.231 55.249 1145 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 7.00 % Allowed : 27.48 % Favored : 65.52 % 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: -2.48 (0.27), residues: 1006 helix: 0.44 (0.51), residues: 117 sheet: -2.07 (0.24), residues: 437 loop : -1.60 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.010 0.001 HIS N 104 PHE 0.016 0.002 PHE B 340 TYR 0.021 0.002 TYR B 342 ARG 0.003 0.001 ARG B 345 *********************** 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 147 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 94 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8099 (tmm) cc_final: 0.7402 (tmm) REVERT: A 2933 CYS cc_start: 0.6534 (OUTLIER) cc_final: 0.5802 (m) REVERT: A 3359 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.4650 (pm20) REVERT: B 360 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6652 (tt0) REVERT: B 426 GLU cc_start: 0.7285 (pp20) cc_final: 0.7020 (pp20) REVERT: B 464 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: H 29 PHE cc_start: 0.8140 (t80) cc_final: 0.7774 (t80) REVERT: H 79 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8393 (tp) REVERT: H 108 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6897 (m-80) outliers start: 53 outliers final: 42 residues processed: 136 average time/residue: 0.1807 time to fit residues: 34.8729 Evaluate side-chains 133 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 3106 ASN Chi-restraints excluded: chain A residue 3164 THR 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 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 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 83 MET 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 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 32 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.111930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.098403 restraints weight = 23310.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.100043 restraints weight = 13929.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.101086 restraints weight = 9838.408| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7638 Z= 0.262 Angle : 0.666 9.941 10408 Z= 0.334 Chirality : 0.044 0.261 1204 Planarity : 0.004 0.051 1357 Dihedral : 6.044 55.141 1145 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 6.47 % Allowed : 28.53 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.27), residues: 1006 helix: 0.62 (0.52), residues: 117 sheet: -2.04 (0.24), residues: 436 loop : -1.54 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.010 0.001 HIS A3114 PHE 0.013 0.001 PHE B 424 TYR 0.020 0.002 TYR A2889 ARG 0.003 0.001 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 149 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8062 (tmm) cc_final: 0.7434 (tmm) REVERT: A 2844 LEU cc_start: 0.7461 (mm) cc_final: 0.7161 (mp) REVERT: A 2933 CYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6725 (m) REVERT: B 360 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6550 (tt0) REVERT: B 464 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: H 79 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8339 (tp) REVERT: H 108 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6738 (m-80) REVERT: N 5 GLN cc_start: 0.4552 (OUTLIER) cc_final: 0.4102 (pm20) outliers start: 49 outliers final: 36 residues processed: 137 average time/residue: 0.1783 time to fit residues: 34.2947 Evaluate side-chains 131 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 89 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3353 ASN 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 367 ILE Chi-restraints excluded: chain B residue 381 PHE 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 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 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 84 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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 = 0.4041 r_free = 0.4041 target = 0.110972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.098938 restraints weight = 23515.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.099165 restraints weight = 16202.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.099649 restraints weight = 13331.070| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7638 Z= 0.315 Angle : 0.701 9.876 10408 Z= 0.355 Chirality : 0.044 0.274 1204 Planarity : 0.004 0.051 1357 Dihedral : 6.206 56.147 1145 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 7.40 % Allowed : 28.14 % Favored : 64.46 % 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: -2.43 (0.27), residues: 1006 helix: 0.51 (0.50), residues: 122 sheet: -2.06 (0.25), residues: 432 loop : -1.57 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.010 0.001 HIS N 104 PHE 0.017 0.002 PHE A3038 TYR 0.025 0.002 TYR B 342 ARG 0.002 0.001 ARG A2836 *********************** 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 149 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 93 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8086 (tmm) cc_final: 0.7415 (tmm) REVERT: A 2933 CYS cc_start: 0.6399 (OUTLIER) cc_final: 0.5884 (m) REVERT: A 3339 TYR cc_start: 0.7060 (t80) cc_final: 0.6818 (t80) REVERT: B 360 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6717 (tt0) REVERT: B 464 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: H 79 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8298 (tp) REVERT: H 108 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6755 (m-80) outliers start: 56 outliers final: 47 residues processed: 138 average time/residue: 0.1735 time to fit residues: 33.8845 Evaluate side-chains 141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 89 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3353 ASN 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 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 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 18 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 22 CYS 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 83 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 0.0970 chunk 7 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3094 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.112600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.099143 restraints weight = 23558.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.100759 restraints weight = 14163.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.101779 restraints weight = 10014.201| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7638 Z= 0.229 Angle : 0.666 10.489 10408 Z= 0.334 Chirality : 0.043 0.268 1204 Planarity : 0.004 0.050 1357 Dihedral : 5.871 54.794 1145 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 6.34 % Allowed : 29.33 % Favored : 64.33 % 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: -2.24 (0.27), residues: 1006 helix: 0.79 (0.51), residues: 121 sheet: -1.95 (0.25), residues: 421 loop : -1.51 (0.28), residues: 464 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 0.015 0.001 PHE B 340 TYR 0.018 0.001 TYR B 425 ARG 0.003 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 146 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8041 (tmm) cc_final: 0.7398 (tmm) REVERT: A 2844 LEU cc_start: 0.7321 (mm) cc_final: 0.7048 (mp) REVERT: A 2933 CYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6811 (m) REVERT: B 341 TRP cc_start: 0.7209 (m100) cc_final: 0.7008 (m100) REVERT: B 360 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6618 (tt0) REVERT: H 79 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8280 (tp) REVERT: H 108 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: L 3 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6536 (mmp) REVERT: N 5 GLN cc_start: 0.4512 (OUTLIER) cc_final: 0.4082 (pm20) outliers start: 48 outliers final: 40 residues processed: 136 average time/residue: 0.1733 time to fit residues: 33.4623 Evaluate side-chains 136 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 90 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3173 VAL Chi-restraints excluded: chain A residue 3353 ASN 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 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 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 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 83 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 79 VAL 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 98 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.112607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.099221 restraints weight = 23469.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.100792 restraints weight = 14236.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.101737 restraints weight = 10109.062| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2256 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= 0.231 Angle : 0.680 11.858 10408 Z= 0.341 Chirality : 0.043 0.262 1204 Planarity : 0.004 0.050 1357 Dihedral : 5.834 55.199 1145 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 6.34 % Allowed : 29.85 % Favored : 63.80 % 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: -2.18 (0.27), residues: 1006 helix: 0.87 (0.52), residues: 121 sheet: -1.90 (0.25), residues: 418 loop : -1.50 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 113 HIS 0.009 0.001 HIS N 104 PHE 0.019 0.001 PHE A3038 TYR 0.019 0.002 TYR A3177 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 145 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8048 (tmm) cc_final: 0.7486 (tmm) REVERT: A 2844 LEU cc_start: 0.7353 (mm) cc_final: 0.7087 (mp) REVERT: A 2933 CYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6840 (m) REVERT: B 360 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6577 (tt0) REVERT: H 79 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8256 (tp) REVERT: H 108 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: N 5 GLN cc_start: 0.5091 (OUTLIER) cc_final: 0.4622 (pm20) outliers start: 48 outliers final: 42 residues processed: 133 average time/residue: 0.1604 time to fit residues: 30.9094 Evaluate side-chains 140 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 93 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3173 VAL Chi-restraints excluded: chain A residue 3353 ASN 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 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 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR 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 83 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 79 VAL 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 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 chunk 50 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.111856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.098594 restraints weight = 23249.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.100132 restraints weight = 14262.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.101125 restraints weight = 10254.576| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2338 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= 0.265 Angle : 0.690 11.971 10408 Z= 0.348 Chirality : 0.043 0.268 1204 Planarity : 0.004 0.051 1357 Dihedral : 5.916 55.490 1145 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 6.74 % Allowed : 29.72 % Favored : 63.54 % 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: -2.17 (0.27), residues: 1006 helix: 0.87 (0.52), residues: 122 sheet: -1.85 (0.25), residues: 431 loop : -1.51 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 113 HIS 0.010 0.001 HIS N 104 PHE 0.014 0.002 PHE B 340 TYR 0.024 0.002 TYR H 80 ARG 0.004 0.001 ARG A2836 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2555.15 seconds wall clock time: 46 minutes 39.53 seconds (2799.53 seconds total)