Starting phenix.real_space_refine on Fri Dec 27 09:20:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz5_15035/12_2024/7zz5_15035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz5_15035/12_2024/7zz5_15035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zz5_15035/12_2024/7zz5_15035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz5_15035/12_2024/7zz5_15035.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz5_15035/12_2024/7zz5_15035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz5_15035/12_2024/7zz5_15035.cif" } resolution = 2.43 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 12 5.16 5 C 2291 2.51 5 N 636 2.21 5 O 691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3633 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3578 Classifications: {'peptide': 461} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 441} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'ACO': 1, 'BCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.26, per 1000 atoms: 0.90 Number of scatterers: 3633 At special positions: 0 Unit cell: (64.66, 73.14, 74.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 3 15.00 O 691 8.00 N 636 7.00 C 2291 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: 1.00 Conformation dependent library (CDL) restraints added in 456.6 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 838 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 5 sheets defined 42.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 removed outlier: 3.516A pdb=" N VAL A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.208A pdb=" N PHE A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 62 through 74 Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.580A pdb=" N TYR A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 190 removed outlier: 3.780A pdb=" N HIS A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 266 Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.124A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.843A pdb=" N GLY A 350 " --> pdb=" O PRO A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 448 through 453 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 4.076A pdb=" N VAL A 30 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 156 Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 288 removed outlier: 6.865A pdb=" N GLU A 274 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 287 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 272 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N HIS A 207 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP A 227 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A 209 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU A 225 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER A 229 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE A 238 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN A 231 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS A 236 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A 237 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 341 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.526A pdb=" N GLY A 356 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 362 172 hydrogen bonds defined for protein. 474 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: 1.07 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 625 1.31 - 1.44: 936 1.44 - 1.57: 2118 1.57 - 1.69: 6 1.69 - 1.82: 18 Bond restraints: 3703 Sorted by residual: bond pdb=" C5A ACO A1201 " pdb=" N7A ACO A1201 " ideal model delta sigma weight residual 1.387 1.520 -0.133 1.00e-02 1.00e+04 1.78e+02 bond pdb=" C6A ACO A1201 " pdb=" N6A ACO A1201 " ideal model delta sigma weight residual 1.337 1.450 -0.113 1.00e-02 1.00e+04 1.29e+02 bond pdb=" C5P ACO A1201 " pdb=" N4P ACO A1201 " ideal model delta sigma weight residual 1.331 1.451 -0.120 1.20e-02 6.94e+03 9.98e+01 bond pdb=" C8A ACO A1201 " pdb=" N9A ACO A1201 " ideal model delta sigma weight residual 1.370 1.270 0.100 1.00e-02 1.00e+04 9.97e+01 bond pdb=" C9P ACO A1201 " pdb=" N8P ACO A1201 " ideal model delta sigma weight residual 1.333 1.453 -0.120 1.30e-02 5.92e+03 8.58e+01 ... (remaining 3698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 4951 3.46 - 6.93: 41 6.93 - 10.39: 15 10.39 - 13.85: 6 13.85 - 17.32: 3 Bond angle restraints: 5016 Sorted by residual: angle pdb=" C4A ACO A1201 " pdb=" N9A ACO A1201 " pdb=" C8A ACO A1201 " ideal model delta sigma weight residual 105.72 122.31 -16.59 1.00e+00 1.00e+00 2.75e+02 angle pdb=" P1A ACO A1201 " pdb=" O3A ACO A1201 " pdb=" P2A ACO A1201 " ideal model delta sigma weight residual 136.83 124.19 12.64 1.00e+00 1.00e+00 1.60e+02 angle pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" CD PRO A 132 " ideal model delta sigma weight residual 112.00 95.76 16.24 1.40e+00 5.10e-01 1.35e+02 angle pdb=" N3A ACO A1201 " pdb=" C4A ACO A1201 " pdb=" N9A ACO A1201 " ideal model delta sigma weight residual 127.04 137.47 -10.43 1.15e+00 7.59e-01 8.26e+01 angle pdb=" C ACO A1201 " pdb=" S1P ACO A1201 " pdb=" C2P ACO A1201 " ideal model delta sigma weight residual 101.25 110.12 -8.87 1.00e+00 1.00e+00 7.87e+01 ... (remaining 5011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 1926 17.67 - 35.33: 222 35.33 - 53.00: 60 53.00 - 70.67: 21 70.67 - 88.34: 11 Dihedral angle restraints: 2240 sinusoidal: 926 harmonic: 1314 Sorted by residual: dihedral pdb=" CA GLU A 175 " pdb=" C GLU A 175 " pdb=" N MET A 176 " pdb=" CA MET A 176 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ILE A 131 " pdb=" C ILE A 131 " pdb=" N PRO A 132 " pdb=" CA PRO A 132 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TYR A 82 " pdb=" C TYR A 82 " pdb=" N GLY A 83 " pdb=" CA GLY A 83 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 429 0.057 - 0.113: 106 0.113 - 0.170: 15 0.170 - 0.226: 1 0.226 - 0.283: 3 Chirality restraints: 554 Sorted by residual: chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3B ACO A1201 " pdb=" C2B ACO A1201 " pdb=" C4B ACO A1201 " pdb=" O3B ACO A1201 " both_signs ideal model delta sigma weight residual False -2.76 -2.49 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C2B ACO A1201 " pdb=" C1B ACO A1201 " pdb=" C3B ACO A1201 " pdb=" O2B ACO A1201 " both_signs ideal model delta sigma weight residual False -2.72 -2.47 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 551 not shown) Planarity restraints: 658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BCT A1202 " 0.084 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" O1 BCT A1202 " -0.031 2.00e-02 2.50e+03 pdb=" O2 BCT A1202 " -0.031 2.00e-02 2.50e+03 pdb=" O3 BCT A1202 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 131 " 0.083 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO A 132 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 459 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C ASP A 459 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP A 459 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 460 " 0.015 2.00e-02 2.50e+03 ... (remaining 655 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 816 2.78 - 3.31: 3348 3.31 - 3.84: 6544 3.84 - 4.37: 7545 4.37 - 4.90: 12734 Nonbonded interactions: 30987 Sorted by model distance: nonbonded pdb=" OE2 GLU A 11 " pdb=" OH TYR A 82 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 329 " pdb=" OE1 GLU A 330 " model vdw 2.332 3.040 nonbonded pdb=" OG1 THR A 296 " pdb=" OE1 GLN A 339 " model vdw 2.333 3.040 nonbonded pdb=" O LYS A 157 " pdb=" NZ LYS A 157 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLU A 46 " pdb=" OH TYR A 48 " model vdw 2.350 3.040 ... (remaining 30982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.410 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.060 Process input model: 14.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 : 0.008 0.173 3703 Z= 0.539 Angle : 1.042 17.316 5016 Z= 0.656 Chirality : 0.052 0.283 554 Planarity : 0.006 0.114 658 Dihedral : 17.808 88.336 1402 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.86 % Allowed : 16.49 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.00 (0.36), residues: 459 helix: -0.40 (0.35), residues: 179 sheet: 0.39 (0.58), residues: 79 loop : -1.26 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 222 PHE 0.028 0.002 PHE A 367 TYR 0.011 0.001 TYR A 82 ARG 0.005 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.445 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 0.8199 time to fit residues: 21.0993 Evaluate side-chains 23 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3703 Z= 0.225 Angle : 0.519 7.911 5016 Z= 0.279 Chirality : 0.044 0.135 554 Planarity : 0.004 0.032 658 Dihedral : 10.677 85.351 565 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.13 % Allowed : 15.69 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.18 (0.39), residues: 459 helix: 0.64 (0.38), residues: 186 sheet: 0.71 (0.61), residues: 78 loop : -1.19 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.015 0.002 PHE A 191 TYR 0.007 0.001 TYR A 48 ARG 0.003 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.353 Fit side-chains REVERT: A 155 MET cc_start: 0.7279 (tmm) cc_final: 0.6764 (tmm) REVERT: A 167 MET cc_start: 0.8028 (tpp) cc_final: 0.7822 (tpt) REVERT: A 196 ILE cc_start: 0.4616 (OUTLIER) cc_final: 0.4208 (mp) REVERT: A 405 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6902 (tmt170) REVERT: A 414 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8217 (t80) outliers start: 8 outliers final: 1 residues processed: 26 average time/residue: 1.0377 time to fit residues: 28.4271 Evaluate side-chains 21 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3703 Z= 0.188 Angle : 0.479 7.119 5016 Z= 0.259 Chirality : 0.044 0.220 554 Planarity : 0.003 0.029 658 Dihedral : 9.523 87.202 558 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.13 % Allowed : 15.69 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.26 (0.39), residues: 459 helix: 1.05 (0.39), residues: 186 sheet: 1.11 (0.63), residues: 71 loop : -1.00 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.015 0.001 PHE A 146 TYR 0.010 0.001 TYR A 48 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.334 Fit side-chains REVERT: A 155 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6619 (tmm) REVERT: A 167 MET cc_start: 0.8058 (tpp) cc_final: 0.7826 (tpt) REVERT: A 196 ILE cc_start: 0.4639 (OUTLIER) cc_final: 0.4241 (mp) REVERT: A 405 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6898 (tmt170) REVERT: A 414 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8251 (t80) outliers start: 8 outliers final: 2 residues processed: 27 average time/residue: 1.0133 time to fit residues: 28.9327 Evaluate side-chains 23 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 224 HIS A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3703 Z= 0.288 Angle : 0.519 6.897 5016 Z= 0.282 Chirality : 0.045 0.154 554 Planarity : 0.003 0.035 658 Dihedral : 9.310 84.095 558 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.66 % Allowed : 16.22 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.32 (0.40), residues: 459 helix: 1.11 (0.39), residues: 188 sheet: 0.80 (0.59), residues: 81 loop : -0.94 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.014 0.002 PHE A 191 TYR 0.016 0.002 TYR A 150 ARG 0.004 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8936 (tp) REVERT: A 155 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6573 (tmm) REVERT: A 167 MET cc_start: 0.8118 (tpp) cc_final: 0.7877 (tpt) REVERT: A 414 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8289 (t80) outliers start: 10 outliers final: 2 residues processed: 32 average time/residue: 1.0698 time to fit residues: 35.8975 Evaluate side-chains 26 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 177 HIS A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3703 Z= 0.232 Angle : 0.508 8.386 5016 Z= 0.272 Chirality : 0.045 0.160 554 Planarity : 0.004 0.057 658 Dihedral : 9.205 82.282 558 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.66 % Allowed : 15.96 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.39 (0.40), residues: 459 helix: 1.26 (0.39), residues: 186 sheet: 0.81 (0.59), residues: 81 loop : -0.97 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 177 PHE 0.009 0.002 PHE A 191 TYR 0.008 0.001 TYR A 48 ARG 0.002 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8922 (tp) REVERT: A 155 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6585 (tmm) REVERT: A 167 MET cc_start: 0.8135 (tpp) cc_final: 0.7911 (tpt) REVERT: A 414 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8334 (t80) outliers start: 10 outliers final: 4 residues processed: 32 average time/residue: 1.0210 time to fit residues: 34.3551 Evaluate side-chains 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 42 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3703 Z= 0.184 Angle : 0.502 9.172 5016 Z= 0.265 Chirality : 0.045 0.157 554 Planarity : 0.003 0.024 658 Dihedral : 8.998 82.232 558 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.60 % Allowed : 17.02 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.44 (0.40), residues: 459 helix: 1.32 (0.39), residues: 186 sheet: 0.86 (0.60), residues: 81 loop : -0.99 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.016 0.001 PHE A 191 TYR 0.007 0.001 TYR A 48 ARG 0.003 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8945 (tp) REVERT: A 155 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6537 (tmm) REVERT: A 167 MET cc_start: 0.8157 (tpp) cc_final: 0.7948 (tpt) REVERT: A 414 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8252 (t80) outliers start: 6 outliers final: 2 residues processed: 28 average time/residue: 1.0223 time to fit residues: 30.1653 Evaluate side-chains 25 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.0770 chunk 17 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.0040 chunk 8 optimal weight: 0.5980 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3703 Z= 0.148 Angle : 0.488 9.302 5016 Z= 0.257 Chirality : 0.044 0.156 554 Planarity : 0.003 0.050 658 Dihedral : 8.748 81.018 558 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.39 % Allowed : 17.02 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.49 (0.40), residues: 459 helix: 1.36 (0.39), residues: 187 sheet: 0.86 (0.60), residues: 82 loop : -0.96 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.007 0.001 PHE A 191 TYR 0.006 0.001 TYR A 82 ARG 0.003 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8985 (tp) REVERT: A 155 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6647 (tmm) REVERT: A 167 MET cc_start: 0.8139 (tpp) cc_final: 0.7927 (tpt) REVERT: A 414 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8217 (t80) outliers start: 9 outliers final: 5 residues processed: 30 average time/residue: 1.1193 time to fit residues: 35.0663 Evaluate side-chains 28 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.3980 chunk 28 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3703 Z= 0.168 Angle : 0.513 11.511 5016 Z= 0.263 Chirality : 0.044 0.157 554 Planarity : 0.003 0.022 658 Dihedral : 8.742 81.456 558 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.13 % Allowed : 17.82 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.54 (0.40), residues: 459 helix: 1.37 (0.39), residues: 187 sheet: 0.91 (0.60), residues: 81 loop : -0.91 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.016 0.001 PHE A 191 TYR 0.007 0.001 TYR A 82 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.8979 (tp) REVERT: A 155 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6648 (tmm) REVERT: A 167 MET cc_start: 0.8180 (tpp) cc_final: 0.7965 (tpt) REVERT: A 414 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8188 (t80) outliers start: 8 outliers final: 5 residues processed: 28 average time/residue: 1.0620 time to fit residues: 31.3096 Evaluate side-chains 28 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 26 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3703 Z= 0.157 Angle : 0.531 14.324 5016 Z= 0.270 Chirality : 0.044 0.155 554 Planarity : 0.003 0.052 658 Dihedral : 8.674 81.472 558 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.39 % Allowed : 17.82 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.52 (0.40), residues: 459 helix: 1.38 (0.39), residues: 187 sheet: 0.87 (0.60), residues: 82 loop : -0.94 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.006 0.001 PHE A 275 TYR 0.006 0.001 TYR A 82 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8967 (tp) REVERT: A 155 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6649 (tmm) REVERT: A 167 MET cc_start: 0.8174 (tpp) cc_final: 0.7969 (tpt) REVERT: A 414 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8182 (t80) outliers start: 9 outliers final: 5 residues processed: 28 average time/residue: 1.0809 time to fit residues: 31.6963 Evaluate side-chains 28 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.0030 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3703 Z= 0.230 Angle : 0.569 16.039 5016 Z= 0.290 Chirality : 0.045 0.169 554 Planarity : 0.003 0.025 658 Dihedral : 8.855 83.239 558 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.86 % Allowed : 18.62 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.57 (0.40), residues: 459 helix: 1.33 (0.39), residues: 187 sheet: 1.27 (0.63), residues: 71 loop : -0.87 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.019 0.002 PHE A 191 TYR 0.008 0.001 TYR A 48 ARG 0.002 0.000 ARG A 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.8975 (tp) REVERT: A 155 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6642 (tmm) REVERT: A 414 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8288 (t80) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.9200 time to fit residues: 27.1369 Evaluate side-chains 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.0000 chunk 31 optimal weight: 0.5980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.064868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053747 restraints weight = 12229.568| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.17 r_work: 0.3055 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3703 Z= 0.191 Angle : 0.578 15.909 5016 Z= 0.289 Chirality : 0.045 0.157 554 Planarity : 0.003 0.052 658 Dihedral : 8.793 82.535 558 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.86 % Allowed : 18.88 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.58 (0.40), residues: 459 helix: 1.33 (0.39), residues: 187 sheet: 1.31 (0.64), residues: 71 loop : -0.86 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.007 0.001 PHE A 275 TYR 0.007 0.001 TYR A 48 ARG 0.002 0.000 ARG A 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.60 seconds wall clock time: 29 minutes 8.61 seconds (1748.61 seconds total)