Starting phenix.real_space_refine on Wed Mar 5 22:17:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz5_15035/03_2025/7zz5_15035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz5_15035/03_2025/7zz5_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_15035/03_2025/7zz5_15035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz5_15035/03_2025/7zz5_15035.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz5_15035/03_2025/7zz5_15035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz5_15035/03_2025/7zz5_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-5624/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: 2.95, per 1000 atoms: 0.81 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: 0.89 Conformation dependent library (CDL) restraints added in 413.8 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: 0.43 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: 1.06 Time building geometry restraints manager: 1.06 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: 1.060 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.350 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 : 0.401 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 0.7568 time to fit residues: 19.5094 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 : 0.443 ------------------------------------------------------------------------------- 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: 0.5980 chunk 41 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.064937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053761 restraints weight = 12472.136| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.19 r_work: 0.3056 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 3703 Z= 0.221 Angle : 0.514 7.868 5016 Z= 0.276 Chirality : 0.044 0.136 554 Planarity : 0.003 0.032 658 Dihedral : 10.601 86.564 565 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.39 % Allowed : 15.43 % 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: -0.15 (0.39), residues: 459 helix: 0.64 (0.38), residues: 187 sheet: 0.88 (0.61), residues: 76 loop : -1.20 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.016 0.002 PHE A 191 TYR 0.006 0.001 TYR A 150 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 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.442 Fit side-chains REVERT: A 155 MET cc_start: 0.7309 (tmm) cc_final: 0.6771 (tmm) REVERT: A 196 ILE cc_start: 0.4720 (OUTLIER) cc_final: 0.4297 (mp) REVERT: A 405 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.7020 (tmt170) REVERT: A 414 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8227 (t80) outliers start: 9 outliers final: 1 residues processed: 27 average time/residue: 1.0798 time to fit residues: 30.6981 Evaluate side-chains 22 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 11 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.064719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053672 restraints weight = 12420.637| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.16 r_work: 0.3052 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3703 Z= 0.200 Angle : 0.485 6.945 5016 Z= 0.262 Chirality : 0.045 0.211 554 Planarity : 0.003 0.029 658 Dihedral : 9.451 86.718 558 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.13 % Allowed : 15.43 % Favored : 82.45 % 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: 0.25 (0.39), residues: 459 helix: 1.05 (0.39), residues: 186 sheet: 1.05 (0.64), residues: 71 loop : -0.99 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.016 0.001 PHE A 146 TYR 0.010 0.001 TYR A 48 ARG 0.001 0.000 ARG A 458 *********************** 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 31 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6725 (tmm) REVERT: A 196 ILE cc_start: 0.4750 (OUTLIER) cc_final: 0.4326 (mp) REVERT: A 414 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8308 (t80) outliers start: 8 outliers final: 2 residues processed: 30 average time/residue: 1.0495 time to fit residues: 33.1372 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 : 0.414 ------------------------------------------------------------------------------- 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 414 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 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 224 HIS A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.064100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.053147 restraints weight = 12545.150| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.18 r_work: 0.3036 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3703 Z= 0.235 Angle : 0.497 7.211 5016 Z= 0.268 Chirality : 0.045 0.163 554 Planarity : 0.003 0.028 658 Dihedral : 9.247 84.008 558 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.39 % Allowed : 16.49 % 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: 0.34 (0.40), residues: 459 helix: 1.15 (0.39), residues: 186 sheet: 0.83 (0.60), residues: 81 loop : -0.95 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.008 0.001 PHE A 42 TYR 0.014 0.001 TYR A 150 ARG 0.003 0.000 ARG A 171 *********************** 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 32 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.8924 (tp) REVERT: A 155 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6718 (tmm) REVERT: A 196 ILE cc_start: 0.5100 (OUTLIER) cc_final: 0.4685 (mp) REVERT: A 414 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8325 (t80) outliers start: 9 outliers final: 3 residues processed: 30 average time/residue: 0.9657 time to fit residues: 30.5444 Evaluate side-chains 28 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain A residue 263 LYS 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 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.063934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.053255 restraints weight = 12568.170| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.08 r_work: 0.3044 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1338 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= 0.243 Angle : 0.513 8.140 5016 Z= 0.273 Chirality : 0.045 0.139 554 Planarity : 0.003 0.028 658 Dihedral : 9.185 82.594 558 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: 0.38 (0.40), residues: 459 helix: 1.20 (0.39), residues: 186 sheet: 0.85 (0.60), residues: 81 loop : -0.95 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 177 PHE 0.014 0.002 PHE A 191 TYR 0.012 0.001 TYR A 150 ARG 0.002 0.000 ARG A 171 *********************** 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 : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8881 (tp) REVERT: A 155 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6741 (tmm) REVERT: A 414 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8341 (t80) outliers start: 10 outliers final: 3 residues processed: 31 average time/residue: 0.9973 time to fit residues: 32.4941 Evaluate side-chains 28 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 414 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 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 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.064210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.053111 restraints weight = 12531.419| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.17 r_work: 0.3034 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1426 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= 0.235 Angle : 0.523 8.613 5016 Z= 0.275 Chirality : 0.045 0.147 554 Planarity : 0.003 0.026 658 Dihedral : 9.126 83.360 558 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.60 % Allowed : 17.29 % 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: 0.41 (0.40), residues: 459 helix: 1.25 (0.39), residues: 186 sheet: 0.88 (0.60), residues: 81 loop : -0.96 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.008 0.002 PHE A 191 TYR 0.010 0.001 TYR A 150 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 30 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8916 (tp) REVERT: A 155 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6679 (tmm) REVERT: A 414 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8387 (t80) outliers start: 6 outliers final: 3 residues processed: 29 average time/residue: 0.9121 time to fit residues: 27.9830 Evaluate side-chains 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 414 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.063750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053019 restraints weight = 12602.634| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.10 r_work: 0.3039 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3703 Z= 0.244 Angle : 0.544 9.276 5016 Z= 0.285 Chirality : 0.045 0.147 554 Planarity : 0.003 0.029 658 Dihedral : 9.154 82.700 558 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.13 % Allowed : 17.02 % Favored : 80.85 % 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: 0.43 (0.40), residues: 459 helix: 1.27 (0.39), residues: 186 sheet: 0.86 (0.59), residues: 81 loop : -0.95 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.015 0.002 PHE A 191 TYR 0.010 0.001 TYR A 150 ARG 0.006 0.000 ARG A 460 *********************** 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 30 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8865 (tp) REVERT: A 155 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6731 (tmm) REVERT: A 414 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8350 (t80) outliers start: 8 outliers final: 4 residues processed: 29 average time/residue: 0.9008 time to fit residues: 27.5583 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 : 0.393 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 29 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.064287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053557 restraints weight = 12587.238| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.10 r_work: 0.3056 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1490 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= 0.187 Angle : 0.523 9.498 5016 Z= 0.274 Chirality : 0.045 0.152 554 Planarity : 0.003 0.023 658 Dihedral : 9.020 82.494 558 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: 0.47 (0.40), residues: 459 helix: 1.29 (0.39), residues: 187 sheet: 0.89 (0.60), residues: 81 loop : -0.92 (0.45), residues: 191 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 0.009 0.001 TYR A 150 ARG 0.003 0.000 ARG A 171 *********************** 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 30 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8896 (tp) REVERT: A 155 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6776 (tmm) REVERT: A 176 MET cc_start: 0.6384 (mmt) cc_final: 0.6081 (mpm) REVERT: A 414 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8291 (t80) outliers start: 8 outliers final: 3 residues processed: 29 average time/residue: 0.8675 time to fit residues: 26.6513 Evaluate side-chains 26 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 15 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 0.0060 overall best weight: 0.2272 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.065514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.054431 restraints weight = 12315.156| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.17 r_work: 0.3075 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3703 Z= 0.138 Angle : 0.525 9.699 5016 Z= 0.272 Chirality : 0.044 0.156 554 Planarity : 0.003 0.022 658 Dihedral : 9.277 88.095 558 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.86 % Allowed : 17.82 % Favored : 80.32 % 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: 0.51 (0.40), residues: 459 helix: 1.36 (0.39), residues: 187 sheet: 0.93 (0.60), residues: 82 loop : -0.95 (0.45), residues: 190 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 0.008 0.001 TYR A 150 ARG 0.013 0.001 ARG A 458 *********************** 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 32 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8915 (tp) REVERT: A 155 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6724 (tmm) REVERT: A 414 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8267 (t80) outliers start: 7 outliers final: 4 residues processed: 31 average time/residue: 1.0046 time to fit residues: 33.0260 Evaluate side-chains 26 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 34 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.065165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.053996 restraints weight = 12500.072| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.19 r_work: 0.3058 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1595 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= 0.184 Angle : 0.563 9.374 5016 Z= 0.294 Chirality : 0.045 0.173 554 Planarity : 0.003 0.022 658 Dihedral : 8.936 86.073 558 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.13 % Allowed : 18.62 % 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: 0.56 (0.40), residues: 459 helix: 1.36 (0.39), residues: 187 sheet: 0.98 (0.61), residues: 81 loop : -0.88 (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 396 TYR 0.008 0.001 TYR A 150 ARG 0.014 0.000 ARG A 458 ********************** 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 31 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8956 (tp) REVERT: A 155 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6674 (tmm) REVERT: A 176 MET cc_start: 0.6608 (mmt) cc_final: 0.6353 (mpm) REVERT: A 414 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8240 (t80) outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.8579 time to fit residues: 27.2771 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 : 0.422 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.064189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.053240 restraints weight = 12671.357| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.10 r_work: 0.3040 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3703 Z= 0.254 Angle : 0.585 9.550 5016 Z= 0.307 Chirality : 0.045 0.165 554 Planarity : 0.003 0.028 658 Dihedral : 9.080 87.331 558 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: 0.57 (0.40), residues: 459 helix: 1.30 (0.39), residues: 187 sheet: 1.28 (0.63), residues: 71 loop : -0.84 (0.44), 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 0.010 0.002 TYR A 150 ARG 0.013 0.001 ARG A 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3043.70 seconds wall clock time: 52 minutes 39.24 seconds (3159.24 seconds total)