Starting phenix.real_space_refine on Fri Dec 27 12:52:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8poc_17788/12_2024/8poc_17788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8poc_17788/12_2024/8poc_17788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8poc_17788/12_2024/8poc_17788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8poc_17788/12_2024/8poc_17788.map" model { file = "/net/cci-nas-00/data/ceres_data/8poc_17788/12_2024/8poc_17788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8poc_17788/12_2024/8poc_17788.cif" } resolution = 4.0 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3108 2.51 5 N 880 2.21 5 O 908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4924 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "B" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "C" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "D" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Time building chain proxies: 3.79, per 1000 atoms: 0.77 Number of scatterers: 4924 At special positions: 0 Unit cell: (86.49, 76.26, 77.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 908 8.00 N 880 7.00 C 3108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 588.4 milliseconds 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 60.1% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 20 through 37 Processing helix chain 'A' and resid 38 through 56 removed outlier: 3.539A pdb=" N ARG A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.100A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 131 removed outlier: 3.896A pdb=" N GLY A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 20 through 37 Processing helix chain 'B' and resid 38 through 56 removed outlier: 3.574A pdb=" N ARG B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 79 removed outlier: 4.039A pdb=" N LEU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 130 Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 20 through 37 Processing helix chain 'C' and resid 38 through 56 removed outlier: 3.596A pdb=" N ARG C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 removed outlier: 4.027A pdb=" N LEU C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 130 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 20 through 37 Processing helix chain 'D' and resid 38 through 56 removed outlier: 3.548A pdb=" N ARG D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 79 removed outlier: 4.039A pdb=" N LEU D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 131 removed outlier: 3.905A pdb=" N GLY D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 82 through 87 Processing sheet with id=AA3, first strand: chain 'C' and resid 82 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 82 through 87 336 hydrogen bonds defined for protein. 966 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: 1.28 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1680 1.34 - 1.46: 1134 1.46 - 1.58: 2174 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 5036 Sorted by residual: bond pdb=" CG1 ILE A 94 " pdb=" CD1 ILE A 94 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.20e+00 bond pdb=" CB GLN B 14 " pdb=" CG GLN B 14 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CG1 ILE D 94 " pdb=" CD1 ILE D 94 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.13e+00 bond pdb=" CB GLN C 14 " pdb=" CG GLN C 14 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CG LEU A 85 " pdb=" CD2 LEU A 85 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.51e-01 ... (remaining 5031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6663 1.71 - 3.41: 129 3.41 - 5.12: 27 5.12 - 6.83: 10 6.83 - 8.53: 3 Bond angle restraints: 6832 Sorted by residual: angle pdb=" C GLN D 16 " pdb=" N LEU D 17 " pdb=" CA LEU D 17 " ideal model delta sigma weight residual 122.31 113.78 8.53 2.34e+00 1.83e-01 1.33e+01 angle pdb=" C GLN C 16 " pdb=" N LEU C 17 " pdb=" CA LEU C 17 " ideal model delta sigma weight residual 122.31 114.00 8.31 2.34e+00 1.83e-01 1.26e+01 angle pdb=" C GLN B 16 " pdb=" N LEU B 17 " pdb=" CA LEU B 17 " ideal model delta sigma weight residual 122.31 114.55 7.76 2.34e+00 1.83e-01 1.10e+01 angle pdb=" CA GLN C 14 " pdb=" CB GLN C 14 " pdb=" CG GLN C 14 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.32e+00 angle pdb=" CA GLN B 14 " pdb=" CB GLN B 14 " pdb=" CG GLN B 14 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.30e+00 ... (remaining 6827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2649 17.13 - 34.26: 276 34.26 - 51.39: 35 51.39 - 68.52: 6 68.52 - 85.65: 18 Dihedral angle restraints: 2984 sinusoidal: 1208 harmonic: 1776 Sorted by residual: dihedral pdb=" CA ASN B 35 " pdb=" C ASN B 35 " pdb=" N ALA B 36 " pdb=" CA ALA B 36 " ideal model delta harmonic sigma weight residual 180.00 -164.77 -15.23 0 5.00e+00 4.00e-02 9.27e+00 dihedral pdb=" CA ARG A 13 " pdb=" CB ARG A 13 " pdb=" CG ARG A 13 " pdb=" CD ARG A 13 " ideal model delta sinusoidal sigma weight residual -60.00 -113.88 53.88 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" CA ARG B 13 " pdb=" CB ARG B 13 " pdb=" CG ARG B 13 " pdb=" CD ARG B 13 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 2981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 569 0.038 - 0.075: 151 0.075 - 0.113: 4 0.113 - 0.150: 0 0.150 - 0.188: 4 Chirality restraints: 728 Sorted by residual: chirality pdb=" CA ILE A 94 " pdb=" N ILE A 94 " pdb=" C ILE A 94 " pdb=" CB ILE A 94 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA ILE D 94 " pdb=" N ILE D 94 " pdb=" C ILE D 94 " pdb=" CB ILE D 94 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA ILE C 94 " pdb=" N ILE C 94 " pdb=" C ILE C 94 " pdb=" CB ILE C 94 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 725 not shown) Planarity restraints: 896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 99 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO C 100 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 100 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 100 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 11 " 0.008 2.00e-02 2.50e+03 1.03e-02 2.11e+00 pdb=" CG TYR B 11 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 11 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 11 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 11 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 11 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 11 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 11 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 99 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO B 100 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " 0.020 5.00e-02 4.00e+02 ... (remaining 893 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1472 2.84 - 3.35: 4800 3.35 - 3.87: 7565 3.87 - 4.38: 7525 4.38 - 4.90: 14384 Nonbonded interactions: 35746 Sorted by model distance: nonbonded pdb=" O GLU D 68 " pdb=" ND2 ASN D 72 " model vdw 2.324 3.120 nonbonded pdb=" N GLU A 89 " pdb=" OE1 GLU A 89 " model vdw 2.340 3.120 nonbonded pdb=" N GLU C 89 " pdb=" OE1 GLU C 89 " model vdw 2.343 3.120 nonbonded pdb=" O GLU B 68 " pdb=" ND2 ASN B 72 " model vdw 2.346 3.120 nonbonded pdb=" NH2 ARG C 112 " pdb=" OE1 GLU C 142 " model vdw 2.382 3.120 ... (remaining 35741 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.810 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 5036 Z= 0.221 Angle : 0.667 8.532 6832 Z= 0.349 Chirality : 0.034 0.188 728 Planarity : 0.004 0.037 896 Dihedral : 14.858 85.653 1848 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 2.14 (0.33), residues: 608 helix: 2.97 (0.27), residues: 344 sheet: 0.47 (0.44), residues: 96 loop : -1.49 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 126 HIS 0.006 0.002 HIS A 96 PHE 0.007 0.001 PHE D 44 TYR 0.025 0.001 TYR B 11 ARG 0.009 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.550 Fit side-chains REVERT: C 93 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8035 (mt-10) REVERT: D 1 MET cc_start: 0.7142 (mpp) cc_final: 0.6579 (mpp) REVERT: D 89 GLU cc_start: 0.8233 (pm20) cc_final: 0.7990 (pm20) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1648 time to fit residues: 28.3381 Evaluate side-chains 108 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS B 104 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5036 Z= 0.272 Angle : 0.588 5.074 6832 Z= 0.298 Chirality : 0.035 0.181 728 Planarity : 0.004 0.034 896 Dihedral : 3.466 15.374 692 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.46 % Allowed : 11.15 % Favored : 85.38 % 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: 2.26 (0.34), residues: 608 helix: 2.93 (0.27), residues: 356 sheet: 0.75 (0.48), residues: 96 loop : -1.59 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 126 HIS 0.003 0.001 HIS B 96 PHE 0.009 0.002 PHE B 25 TYR 0.006 0.001 TYR B 95 ARG 0.003 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.504 Fit side-chains REVERT: A 93 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8130 (mt-10) REVERT: B 1 MET cc_start: 0.7368 (mmm) cc_final: 0.7113 (mpp) REVERT: B 68 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8148 (pt0) REVERT: B 93 GLU cc_start: 0.8455 (tt0) cc_final: 0.7911 (mt-10) REVERT: C 93 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8055 (mt-10) REVERT: D 1 MET cc_start: 0.7783 (mpp) cc_final: 0.7581 (mpp) outliers start: 18 outliers final: 11 residues processed: 135 average time/residue: 0.1759 time to fit residues: 29.8841 Evaluate side-chains 134 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 0.0980 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS C 96 HIS ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5036 Z= 0.241 Angle : 0.554 4.553 6832 Z= 0.279 Chirality : 0.034 0.173 728 Planarity : 0.004 0.034 896 Dihedral : 3.407 15.214 692 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.08 % Allowed : 16.15 % Favored : 80.77 % 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: 2.44 (0.34), residues: 608 helix: 3.05 (0.27), residues: 356 sheet: 0.78 (0.47), residues: 96 loop : -1.42 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 21 HIS 0.005 0.001 HIS B 79 PHE 0.007 0.001 PHE A 25 TYR 0.011 0.001 TYR B 11 ARG 0.003 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.584 Fit side-chains REVERT: A 15 GLN cc_start: 0.8704 (tp40) cc_final: 0.8451 (tp40) REVERT: A 93 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8144 (mt-10) REVERT: B 93 GLU cc_start: 0.8493 (tt0) cc_final: 0.8050 (mt-10) REVERT: C 93 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8084 (mt-10) REVERT: D 1 MET cc_start: 0.7923 (mpp) cc_final: 0.7626 (mpp) REVERT: D 68 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: D 89 GLU cc_start: 0.8281 (pm20) cc_final: 0.8038 (pm20) outliers start: 16 outliers final: 8 residues processed: 127 average time/residue: 0.1678 time to fit residues: 26.9889 Evaluate side-chains 129 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5036 Z= 0.423 Angle : 0.660 5.975 6832 Z= 0.333 Chirality : 0.037 0.167 728 Planarity : 0.004 0.033 896 Dihedral : 3.730 16.606 692 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.58 % Allowed : 16.54 % Favored : 77.88 % 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 (0.34), residues: 608 helix: 2.73 (0.26), residues: 356 sheet: 0.74 (0.46), residues: 96 loop : -1.21 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 111 HIS 0.007 0.001 HIS D 96 PHE 0.011 0.002 PHE D 25 TYR 0.009 0.002 TYR D 95 ARG 0.003 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.622 Fit side-chains REVERT: A 17 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8627 (pp) REVERT: A 68 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: B 17 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8630 (pp) REVERT: B 93 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: D 17 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8601 (pp) REVERT: D 68 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8114 (pt0) outliers start: 29 outliers final: 17 residues processed: 132 average time/residue: 0.1495 time to fit residues: 25.7971 Evaluate side-chains 140 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5036 Z= 0.188 Angle : 0.551 6.491 6832 Z= 0.271 Chirality : 0.034 0.177 728 Planarity : 0.004 0.036 896 Dihedral : 3.372 15.161 692 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.00 % Allowed : 18.46 % Favored : 76.54 % 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: 2.67 (0.34), residues: 608 helix: 3.16 (0.26), residues: 356 sheet: 0.75 (0.45), residues: 96 loop : -1.05 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 111 HIS 0.003 0.001 HIS B 96 PHE 0.004 0.001 PHE D 151 TYR 0.015 0.001 TYR C 11 ARG 0.003 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.778 Fit side-chains REVERT: A 17 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8519 (pp) REVERT: A 93 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8210 (mt-10) REVERT: B 93 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: C 17 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8522 (pp) REVERT: D 17 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8503 (pp) REVERT: D 68 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: D 89 GLU cc_start: 0.8294 (pm20) cc_final: 0.8002 (pm20) outliers start: 26 outliers final: 12 residues processed: 129 average time/residue: 0.1577 time to fit residues: 26.3705 Evaluate side-chains 130 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5036 Z= 0.245 Angle : 0.563 6.499 6832 Z= 0.276 Chirality : 0.034 0.183 728 Planarity : 0.004 0.035 896 Dihedral : 3.318 14.966 692 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.81 % Allowed : 19.04 % Favored : 76.15 % 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: 2.72 (0.34), residues: 608 helix: 3.17 (0.26), residues: 356 sheet: 0.82 (0.46), residues: 96 loop : -0.97 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 111 HIS 0.003 0.001 HIS B 79 PHE 0.007 0.001 PHE C 78 TYR 0.010 0.001 TYR A 11 ARG 0.004 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.635 Fit side-chains REVERT: A 17 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8538 (pp) REVERT: B 93 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: C 17 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8596 (pp) REVERT: D 17 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8520 (pp) REVERT: D 68 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8069 (pt0) outliers start: 25 outliers final: 15 residues processed: 125 average time/residue: 0.1663 time to fit residues: 26.7318 Evaluate side-chains 131 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5036 Z= 0.213 Angle : 0.558 7.514 6832 Z= 0.272 Chirality : 0.033 0.184 728 Planarity : 0.004 0.035 896 Dihedral : 3.267 14.627 692 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.38 % Allowed : 18.08 % Favored : 76.54 % 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: 2.80 (0.34), residues: 608 helix: 3.25 (0.26), residues: 356 sheet: 0.80 (0.44), residues: 96 loop : -0.94 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 21 HIS 0.003 0.001 HIS B 79 PHE 0.006 0.001 PHE C 44 TYR 0.009 0.001 TYR D 11 ARG 0.003 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.649 Fit side-chains REVERT: A 17 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8512 (pp) REVERT: B 17 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8523 (pp) REVERT: B 93 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: C 17 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8549 (pp) REVERT: C 152 ARG cc_start: 0.8727 (tpp80) cc_final: 0.8208 (mtt90) REVERT: D 17 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8510 (pp) outliers start: 28 outliers final: 14 residues processed: 132 average time/residue: 0.1528 time to fit residues: 25.9993 Evaluate side-chains 133 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5036 Z= 0.214 Angle : 0.565 8.020 6832 Z= 0.274 Chirality : 0.034 0.183 728 Planarity : 0.004 0.035 896 Dihedral : 3.242 14.530 692 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.19 % Allowed : 17.88 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.34), residues: 608 helix: 3.29 (0.26), residues: 356 sheet: 0.80 (0.44), residues: 96 loop : -0.82 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 111 HIS 0.003 0.001 HIS B 79 PHE 0.005 0.001 PHE B 78 TYR 0.009 0.001 TYR D 11 ARG 0.004 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.584 Fit side-chains REVERT: A 17 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8520 (pp) REVERT: B 17 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8524 (pp) REVERT: B 93 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: C 17 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8557 (pp) REVERT: D 17 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8501 (pp) REVERT: D 68 GLU cc_start: 0.8273 (pt0) cc_final: 0.8061 (pt0) outliers start: 27 outliers final: 16 residues processed: 130 average time/residue: 0.1603 time to fit residues: 26.7228 Evaluate side-chains 132 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.0270 chunk 47 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5036 Z= 0.186 Angle : 0.564 8.271 6832 Z= 0.272 Chirality : 0.033 0.181 728 Planarity : 0.004 0.035 896 Dihedral : 3.206 14.083 692 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.38 % Allowed : 18.08 % Favored : 76.54 % 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: 2.89 (0.34), residues: 608 helix: 3.32 (0.27), residues: 356 sheet: 0.77 (0.43), residues: 96 loop : -0.85 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 111 HIS 0.003 0.001 HIS B 96 PHE 0.005 0.001 PHE D 44 TYR 0.016 0.001 TYR A 123 ARG 0.008 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.523 Fit side-chains REVERT: A 17 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8492 (pp) REVERT: B 17 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8541 (pp) REVERT: B 93 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: C 17 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8521 (pp) REVERT: C 152 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8220 (mtt90) REVERT: D 15 GLN cc_start: 0.8688 (tp40) cc_final: 0.8462 (mt0) REVERT: D 17 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8484 (pp) outliers start: 28 outliers final: 18 residues processed: 129 average time/residue: 0.1730 time to fit residues: 28.8753 Evaluate side-chains 131 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5036 Z= 0.212 Angle : 0.588 8.576 6832 Z= 0.283 Chirality : 0.034 0.180 728 Planarity : 0.004 0.036 896 Dihedral : 3.208 14.368 692 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.62 % Allowed : 17.88 % Favored : 77.50 % 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: 2.93 (0.34), residues: 608 helix: 3.31 (0.27), residues: 356 sheet: 0.86 (0.44), residues: 96 loop : -0.77 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 21 HIS 0.003 0.001 HIS B 79 PHE 0.006 0.001 PHE D 44 TYR 0.017 0.001 TYR B 123 ARG 0.005 0.000 ARG B 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.557 Fit side-chains REVERT: A 17 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8524 (pp) REVERT: B 17 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8548 (pp) REVERT: B 93 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: C 17 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8546 (pp) REVERT: C 152 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8204 (mtt90) REVERT: D 15 GLN cc_start: 0.8679 (tp40) cc_final: 0.8447 (mt0) REVERT: D 17 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8514 (pp) outliers start: 24 outliers final: 18 residues processed: 133 average time/residue: 0.1586 time to fit residues: 27.3279 Evaluate side-chains 136 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.156080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113113 restraints weight = 6753.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115459 restraints weight = 5549.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117062 restraints weight = 4878.185| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5036 Z= 0.237 Angle : 0.615 8.441 6832 Z= 0.298 Chirality : 0.034 0.177 728 Planarity : 0.004 0.036 896 Dihedral : 3.240 14.208 692 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.00 % Allowed : 18.08 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.34), residues: 608 helix: 3.31 (0.27), residues: 356 sheet: 0.86 (0.44), residues: 96 loop : -0.78 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 21 HIS 0.004 0.001 HIS A 79 PHE 0.005 0.001 PHE C 78 TYR 0.023 0.001 TYR D 123 ARG 0.004 0.000 ARG B 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.18 seconds wall clock time: 25 minutes 6.03 seconds (1506.03 seconds total)