Starting phenix.real_space_refine on Fri Dec 27 20:33:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v8s_43044/12_2024/8v8s_43044.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v8s_43044/12_2024/8v8s_43044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v8s_43044/12_2024/8v8s_43044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v8s_43044/12_2024/8v8s_43044.map" model { file = "/net/cci-nas-00/data/ceres_data/8v8s_43044/12_2024/8v8s_43044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v8s_43044/12_2024/8v8s_43044.cif" } resolution = 2.2 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= -0.002 sd= 0.065 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 52 5.16 5 C 4368 2.51 5 N 1060 2.21 5 O 1237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6717 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Restraints were copied for chains: C, B, D Time building chain proxies: 3.51, per 1000 atoms: 0.52 Number of scatterers: 6717 At special positions: 0 Unit cell: (77.562, 77.562, 67.554, 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 52 16.00 O 1237 8.00 N 1060 7.00 C 4368 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: 1.59 Conformation dependent library (CDL) restraints added in 986.9 milliseconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 73.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 32 through 56 removed outlier: 3.644A pdb=" N THR A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 111 through 137 removed outlier: 3.567A pdb=" N PHE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 213 through 225 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 231 through 251 Proline residue: A 237 - end of helix Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.644A pdb=" N THR B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 111 through 137 removed outlier: 3.567A pdb=" N PHE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 178 Processing helix chain 'B' and resid 188 through 205 Processing helix chain 'B' and resid 213 through 225 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 231 through 251 Proline residue: B 237 - end of helix Processing helix chain 'C' and resid 33 through 56 removed outlier: 3.644A pdb=" N THR C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.567A pdb=" N PHE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 178 Processing helix chain 'C' and resid 188 through 205 Processing helix chain 'C' and resid 213 through 225 Proline residue: C 220 - end of helix Processing helix chain 'C' and resid 231 through 251 Proline residue: C 237 - end of helix Processing helix chain 'D' and resid 33 through 56 removed outlier: 3.644A pdb=" N THR D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 111 through 137 removed outlier: 3.568A pdb=" N PHE D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 178 Processing helix chain 'D' and resid 188 through 205 Processing helix chain 'D' and resid 213 through 225 Proline residue: D 220 - end of helix Processing helix chain 'D' and resid 231 through 251 Proline residue: D 237 - end of helix 485 hydrogen bonds defined for protein. 1455 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: 1.56 Time building geometry restraints manager: 1.84 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: 2016 1.34 - 1.46: 1641 1.46 - 1.58: 3051 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 6788 Sorted by residual: bond pdb=" N MET C 212 " pdb=" CA MET C 212 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.48e-02 4.57e+03 7.57e-01 bond pdb=" N MET D 212 " pdb=" CA MET D 212 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.48e-02 4.57e+03 7.55e-01 bond pdb=" N MET A 212 " pdb=" CA MET A 212 " ideal model delta sigma weight residual 1.462 1.474 -0.013 1.48e-02 4.57e+03 7.37e-01 bond pdb=" N MET B 212 " pdb=" CA MET B 212 " ideal model delta sigma weight residual 1.462 1.474 -0.013 1.48e-02 4.57e+03 7.37e-01 bond pdb=" CB ASN C 226 " pdb=" CG ASN C 226 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.35e-01 ... (remaining 6783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 9017 1.16 - 2.32: 187 2.32 - 3.48: 44 3.48 - 4.64: 8 4.64 - 5.80: 12 Bond angle restraints: 9268 Sorted by residual: angle pdb=" C SER C 211 " pdb=" N MET C 212 " pdb=" CA MET C 212 " ideal model delta sigma weight residual 122.61 125.79 -3.18 1.56e+00 4.11e-01 4.17e+00 angle pdb=" C SER D 211 " pdb=" N MET D 212 " pdb=" CA MET D 212 " ideal model delta sigma weight residual 122.61 125.78 -3.17 1.56e+00 4.11e-01 4.13e+00 angle pdb=" C TYR B 250 " pdb=" N VAL B 251 " pdb=" CA VAL B 251 " ideal model delta sigma weight residual 123.16 121.01 2.15 1.06e+00 8.90e-01 4.12e+00 angle pdb=" C SER A 211 " pdb=" N MET A 212 " pdb=" CA MET A 212 " ideal model delta sigma weight residual 122.61 125.77 -3.16 1.56e+00 4.11e-01 4.11e+00 angle pdb=" C TYR A 250 " pdb=" N VAL A 251 " pdb=" CA VAL A 251 " ideal model delta sigma weight residual 123.16 121.01 2.15 1.06e+00 8.90e-01 4.10e+00 ... (remaining 9263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.10: 3215 11.10 - 22.19: 369 22.19 - 33.29: 124 33.29 - 44.39: 76 44.39 - 55.48: 48 Dihedral angle restraints: 3832 sinusoidal: 1344 harmonic: 2488 Sorted by residual: dihedral pdb=" CA PHE D 203 " pdb=" C PHE D 203 " pdb=" N ALA D 204 " pdb=" CA ALA D 204 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE A 203 " pdb=" C PHE A 203 " pdb=" N ALA A 204 " pdb=" CA ALA A 204 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE B 203 " pdb=" C PHE B 203 " pdb=" N ALA B 204 " pdb=" CA ALA B 204 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 3829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 598 0.023 - 0.046: 266 0.046 - 0.069: 173 0.069 - 0.092: 42 0.092 - 0.114: 33 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA PRO D 237 " pdb=" N PRO D 237 " pdb=" C PRO D 237 " pdb=" CB PRO D 237 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" C PRO A 237 " pdb=" CB PRO A 237 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.01e-01 chirality pdb=" CA MET C 212 " pdb=" N MET C 212 " pdb=" C MET C 212 " pdb=" CB MET C 212 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.00e-01 ... (remaining 1109 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 236 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO B 237 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 237 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 237 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 236 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 237 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 236 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO D 237 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 237 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 237 " -0.018 5.00e-02 4.00e+02 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 557 2.74 - 3.28: 7142 3.28 - 3.82: 12239 3.82 - 4.36: 14558 4.36 - 4.90: 24304 Nonbonded interactions: 58800 Sorted by model distance: nonbonded pdb=" O HOH A 407 " pdb=" O HOH A 419 " model vdw 2.203 3.040 nonbonded pdb=" O HOH B 407 " pdb=" O HOH B 419 " model vdw 2.203 3.040 nonbonded pdb=" O HOH C 407 " pdb=" O HOH C 419 " model vdw 2.203 3.040 nonbonded pdb=" O HOH D 407 " pdb=" O HOH D 419 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG C 108 " pdb=" OH TYR C 250 " model vdw 2.308 3.120 ... (remaining 58795 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 individual isotropic 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.030 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.002 0.018 6788 Z= 0.114 Angle : 0.472 5.805 9268 Z= 0.246 Chirality : 0.037 0.114 1112 Planarity : 0.004 0.033 1132 Dihedral : 14.020 55.483 2256 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % 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: 0.33 (0.27), residues: 884 helix: 0.29 (0.21), residues: 584 sheet: None (None), residues: 0 loop : 0.40 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 59 HIS 0.002 0.001 HIS A 230 PHE 0.007 0.001 PHE C 168 TYR 0.004 0.001 TYR B 233 ARG 0.002 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.6827 (mtm-85) REVERT: B 250 TYR cc_start: 0.8740 (m-10) cc_final: 0.8355 (m-80) REVERT: C 108 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.6821 (mtm-85) REVERT: C 250 TYR cc_start: 0.8738 (m-10) cc_final: 0.8357 (m-80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.8994 time to fit residues: 134.6832 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6788 Z= 0.242 Angle : 0.603 7.657 9268 Z= 0.320 Chirality : 0.042 0.148 1112 Planarity : 0.005 0.033 1132 Dihedral : 4.197 21.009 924 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.87 % Allowed : 11.21 % Favored : 85.92 % 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: 1.45 (0.27), residues: 884 helix: 1.39 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.19 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 35 HIS 0.003 0.001 HIS D 201 PHE 0.007 0.001 PHE B 48 TYR 0.008 0.002 TYR B 233 ARG 0.004 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.207 Fit side-chains REVERT: A 108 ARG cc_start: 0.7519 (mtm-85) cc_final: 0.7073 (mpt90) REVERT: B 108 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.7078 (mpt90) REVERT: C 108 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.7078 (mpt90) REVERT: D 108 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.7074 (mpt90) outliers start: 20 outliers final: 16 residues processed: 122 average time/residue: 1.2489 time to fit residues: 161.9591 Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6788 Z= 0.187 Angle : 0.553 6.952 9268 Z= 0.291 Chirality : 0.040 0.109 1112 Planarity : 0.004 0.034 1132 Dihedral : 4.089 20.602 924 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.87 % Allowed : 11.64 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.28), residues: 884 helix: 1.78 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.13 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 35 HIS 0.002 0.001 HIS A 201 PHE 0.006 0.001 PHE A 168 TYR 0.007 0.001 TYR C 233 ARG 0.002 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.774 Fit side-chains REVERT: A 108 ARG cc_start: 0.7448 (mtm-85) cc_final: 0.6930 (mpt180) REVERT: B 108 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.6922 (mpt180) REVERT: C 108 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.6917 (mpt180) REVERT: D 108 ARG cc_start: 0.7449 (mtm-85) cc_final: 0.6932 (mpt180) outliers start: 20 outliers final: 16 residues processed: 129 average time/residue: 1.2742 time to fit residues: 173.1026 Evaluate side-chains 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 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 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6788 Z= 0.177 Angle : 0.540 6.615 9268 Z= 0.282 Chirality : 0.040 0.108 1112 Planarity : 0.004 0.035 1132 Dihedral : 4.056 20.882 924 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.45 % Allowed : 10.49 % Favored : 86.06 % 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: 2.01 (0.28), residues: 884 helix: 1.92 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.12 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 35 HIS 0.003 0.001 HIS A 201 PHE 0.006 0.001 PHE D 218 TYR 0.007 0.001 TYR D 233 ARG 0.002 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.700 Fit side-chains REVERT: A 108 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7110 (mtm-85) REVERT: B 108 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7112 (mtm-85) REVERT: C 108 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6896 (mpt90) REVERT: D 108 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7116 (mtm-85) outliers start: 24 outliers final: 16 residues processed: 121 average time/residue: 1.1783 time to fit residues: 150.8293 Evaluate side-chains 126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.003 0.032 6788 Z= 0.193 Angle : 0.549 6.672 9268 Z= 0.287 Chirality : 0.040 0.108 1112 Planarity : 0.004 0.035 1132 Dihedral : 4.096 21.603 924 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.30 % Allowed : 11.78 % Favored : 84.91 % 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: 2.02 (0.28), residues: 884 helix: 1.94 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.09 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 35 HIS 0.003 0.001 HIS B 201 PHE 0.006 0.001 PHE D 218 TYR 0.008 0.001 TYR A 233 ARG 0.002 0.001 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.789 Fit side-chains REVERT: A 108 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7115 (mtm-85) REVERT: B 108 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7106 (mtm-85) REVERT: C 108 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6926 (mpt90) REVERT: D 108 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7127 (mtm-85) outliers start: 23 outliers final: 16 residues processed: 119 average time/residue: 1.2588 time to fit residues: 158.0310 Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6788 Z= 0.184 Angle : 0.547 6.632 9268 Z= 0.285 Chirality : 0.040 0.108 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.079 21.582 924 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.02 % Allowed : 12.07 % Favored : 84.91 % 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: 2.02 (0.28), residues: 884 helix: 1.96 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.04 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 35 HIS 0.003 0.001 HIS D 201 PHE 0.006 0.001 PHE A 218 TYR 0.008 0.001 TYR A 233 ARG 0.002 0.001 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.791 Fit side-chains REVERT: A 108 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7121 (mtm-85) REVERT: B 108 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7120 (mtm-85) REVERT: C 108 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6927 (mpt90) REVERT: D 108 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7119 (mtm-85) outliers start: 21 outliers final: 16 residues processed: 120 average time/residue: 1.2335 time to fit residues: 156.1903 Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6788 Z= 0.287 Angle : 0.620 7.203 9268 Z= 0.326 Chirality : 0.043 0.113 1112 Planarity : 0.005 0.038 1132 Dihedral : 4.345 23.378 924 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.72 % Allowed : 14.37 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.28), residues: 884 helix: 1.77 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.08 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 35 HIS 0.004 0.001 HIS D 201 PHE 0.010 0.002 PHE B 48 TYR 0.011 0.002 TYR B 207 ARG 0.002 0.001 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.760 Fit side-chains REVERT: A 108 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.7200 (mtm180) REVERT: B 108 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7188 (mtm180) REVERT: C 108 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.7187 (mtm180) REVERT: D 108 ARG cc_start: 0.7479 (mtm-85) cc_final: 0.7201 (mtm180) outliers start: 12 outliers final: 12 residues processed: 110 average time/residue: 1.1723 time to fit residues: 136.5237 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.0770 chunk 74 optimal weight: 0.7980 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6788 Z= 0.153 Angle : 0.534 6.443 9268 Z= 0.275 Chirality : 0.039 0.110 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.008 20.589 924 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.72 % Allowed : 14.22 % Favored : 84.05 % 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: 2.03 (0.28), residues: 884 helix: 2.00 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.04 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 35 HIS 0.002 0.000 HIS C 201 PHE 0.008 0.001 PHE D 168 TYR 0.006 0.001 TYR C 233 ARG 0.002 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.861 Fit side-chains REVERT: A 108 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7121 (mtm-85) REVERT: B 108 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7120 (mtm-85) REVERT: C 108 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7124 (mtm-85) REVERT: D 108 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7119 (mtm-85) outliers start: 12 outliers final: 8 residues processed: 120 average time/residue: 1.3757 time to fit residues: 173.8731 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6788 Z= 0.175 Angle : 0.559 6.460 9268 Z= 0.287 Chirality : 0.040 0.110 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.044 21.492 924 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.30 % Allowed : 15.09 % Favored : 82.61 % 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: 2.00 (0.28), residues: 884 helix: 2.00 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.11 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 35 HIS 0.003 0.001 HIS D 201 PHE 0.007 0.001 PHE D 168 TYR 0.007 0.001 TYR C 233 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.826 Fit side-chains REVERT: A 108 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7114 (mtm-85) REVERT: B 108 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7111 (mtm-85) REVERT: C 108 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7113 (mtm-85) REVERT: D 108 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7112 (mtm-85) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 1.1641 time to fit residues: 142.5524 Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 0.0370 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6788 Z= 0.181 Angle : 0.577 6.422 9268 Z= 0.295 Chirality : 0.040 0.111 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.094 21.559 924 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.30 % Allowed : 14.94 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.28), residues: 884 helix: 1.91 (0.20), residues: 608 sheet: None (None), residues: 0 loop : -0.06 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 35 HIS 0.003 0.001 HIS B 201 PHE 0.007 0.001 PHE D 48 TYR 0.007 0.001 TYR B 233 ARG 0.002 0.000 ARG D 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.649 Fit side-chains REVERT: A 108 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7117 (mtm-85) REVERT: B 108 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7114 (mtm-85) REVERT: C 108 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7114 (mtm-85) REVERT: D 108 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7114 (mtm-85) outliers start: 16 outliers final: 12 residues processed: 112 average time/residue: 1.2131 time to fit residues: 143.1953 Evaluate side-chains 118 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.0270 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5487 r_free = 0.5487 target = 0.263423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5412 r_free = 0.5412 target = 0.247464 restraints weight = 6256.348| |-----------------------------------------------------------------------------| r_work (start): 0.5400 rms_B_bonded: 1.63 r_work: 0.5392 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.5282 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.5282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6788 Z= 0.195 Angle : 0.601 6.715 9268 Z= 0.306 Chirality : 0.040 0.112 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.154 21.867 924 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.30 % Allowed : 15.52 % Favored : 82.18 % 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: 1.89 (0.28), residues: 884 helix: 1.89 (0.20), residues: 608 sheet: None (None), residues: 0 loop : -0.13 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 35 HIS 0.003 0.001 HIS D 201 PHE 0.007 0.001 PHE C 48 TYR 0.008 0.001 TYR B 233 ARG 0.002 0.000 ARG A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2800.92 seconds wall clock time: 51 minutes 38.47 seconds (3098.47 seconds total)