Starting phenix.real_space_refine on Mon Feb 10 19:34:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w77_37336/02_2025/8w77_37336_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w77_37336/02_2025/8w77_37336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w77_37336/02_2025/8w77_37336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w77_37336/02_2025/8w77_37336.map" model { file = "/net/cci-nas-00/data/ceres_data/8w77_37336/02_2025/8w77_37336_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w77_37336/02_2025/8w77_37336_neut.cif" } resolution = 3.61 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= -0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 4 5.16 5 C 1043 2.51 5 N 274 2.21 5 O 280 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-5592/modules/chem_data/mon_lib" Total number of atoms: 1601 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1601 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 14, 'TRANS': 245} Chain breaks: 5 Unresolved non-hydrogen bonds: 483 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 399 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 191 Time building chain proxies: 2.24, per 1000 atoms: 1.40 Number of scatterers: 1601 At special positions: 0 Unit cell: (60.208, 59.36, 75.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 4 16.00 O 280 8.00 N 274 7.00 C 1043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 181 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 251.5 milliseconds 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 498 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 1 sheets defined 83.5% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 29 through 52 removed outlier: 4.341A pdb=" N PHE A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 77 Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.637A pdb=" N MET A 83 " --> pdb=" O THR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 130 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 139 through 159 Processing helix chain 'A' and resid 159 through 168 removed outlier: 4.117A pdb=" N PHE A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 removed outlier: 3.673A pdb=" N LYS A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 209 removed outlier: 3.820A pdb=" N TYR A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 3.635A pdb=" N ILE A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.620A pdb=" N THR A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 242' Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.641A pdb=" N ILE A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 271 through 294 removed outlier: 3.587A pdb=" N HIS A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Proline residue: A 286 - end of helix Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 8.868A pdb=" N ILE A 176 " --> pdb=" O SER A 13 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU A 15 " --> pdb=" O ILE A 176 " (cutoff:3.500A) 142 hydrogen bonds defined for protein. 426 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: 0.44 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 418 1.33 - 1.45: 269 1.45 - 1.57: 944 1.57 - 1.69: 0 1.69 - 1.80: 4 Bond restraints: 1635 Sorted by residual: bond pdb=" N PRO A 11 " pdb=" CD PRO A 11 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" C MET A 112 " pdb=" O MET A 112 " ideal model delta sigma weight residual 1.237 1.217 0.019 1.19e-02 7.06e+03 2.66e+00 bond pdb=" C MET A 112 " pdb=" N GLU A 113 " ideal model delta sigma weight residual 1.335 1.316 0.019 1.31e-02 5.83e+03 2.00e+00 bond pdb=" C LEU A 156 " pdb=" O LEU A 156 " ideal model delta sigma weight residual 1.237 1.220 0.016 1.17e-02 7.31e+03 1.94e+00 bond pdb=" N MET A 112 " pdb=" CA MET A 112 " ideal model delta sigma weight residual 1.459 1.444 0.015 1.23e-02 6.61e+03 1.45e+00 ... (remaining 1630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 2179 1.52 - 3.03: 64 3.03 - 4.55: 9 4.55 - 6.06: 8 6.06 - 7.58: 3 Bond angle restraints: 2263 Sorted by residual: angle pdb=" N ILE A 159 " pdb=" CA ILE A 159 " pdb=" C ILE A 159 " ideal model delta sigma weight residual 108.88 116.46 -7.58 2.16e+00 2.14e-01 1.23e+01 angle pdb=" CA PRO A 11 " pdb=" N PRO A 11 " pdb=" CD PRO A 11 " ideal model delta sigma weight residual 112.00 107.30 4.70 1.40e+00 5.10e-01 1.13e+01 angle pdb=" N VAL A 209 " pdb=" CA VAL A 209 " pdb=" C VAL A 209 " ideal model delta sigma weight residual 112.12 109.39 2.73 8.40e-01 1.42e+00 1.06e+01 angle pdb=" N LEU A 138 " pdb=" CA LEU A 138 " pdb=" C LEU A 138 " ideal model delta sigma weight residual 108.73 104.41 4.32 1.63e+00 3.76e-01 7.03e+00 angle pdb=" CA ARG A 225 " pdb=" C ARG A 225 " pdb=" N ALA A 226 " ideal model delta sigma weight residual 118.14 114.70 3.44 1.31e+00 5.83e-01 6.89e+00 ... (remaining 2258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.17: 854 9.17 - 18.35: 46 18.35 - 27.52: 25 27.52 - 36.70: 16 36.70 - 45.87: 3 Dihedral angle restraints: 944 sinusoidal: 183 harmonic: 761 Sorted by residual: dihedral pdb=" CB CYS A 99 " pdb=" SG CYS A 99 " pdb=" SG CYS A 181 " pdb=" CB CYS A 181 " ideal model delta sinusoidal sigma weight residual -86.00 -118.22 32.22 1 1.00e+01 1.00e-02 1.48e+01 dihedral pdb=" CA LEU A 164 " pdb=" CB LEU A 164 " pdb=" CG LEU A 164 " pdb=" CD1 LEU A 164 " ideal model delta sinusoidal sigma weight residual 180.00 137.85 42.15 3 1.50e+01 4.44e-03 7.56e+00 dihedral pdb=" SG CYS A 99 " pdb=" CB CYS A 181 " pdb=" SG CYS A 181 " pdb=" CA CYS A 181 " ideal model delta sinusoidal sigma weight residual 183.00 140.82 42.18 1 2.00e+01 2.50e-03 6.21e+00 ... (remaining 941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 182 0.040 - 0.080: 76 0.080 - 0.120: 22 0.120 - 0.160: 5 0.160 - 0.200: 2 Chirality restraints: 287 Sorted by residual: chirality pdb=" CA ALA A 226 " pdb=" N ALA A 226 " pdb=" C ALA A 226 " pdb=" CB ALA A 226 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA LEU A 237 " pdb=" N LEU A 237 " pdb=" C LEU A 237 " pdb=" CB LEU A 237 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA LEU A 138 " pdb=" N LEU A 138 " pdb=" C LEU A 138 " pdb=" CB LEU A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 284 not shown) Planarity restraints: 298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 225 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C ARG A 225 " 0.059 2.00e-02 2.50e+03 pdb=" O ARG A 225 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA A 226 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 159 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 160 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 160 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 160 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 287 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.031 5.00e-02 4.00e+02 ... (remaining 295 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 734 2.95 - 3.44: 1732 3.44 - 3.93: 2396 3.93 - 4.41: 2364 4.41 - 4.90: 4134 Nonbonded interactions: 11360 Sorted by model distance: nonbonded pdb=" O THR A 135 " pdb=" O LEU A 138 " model vdw 2.463 3.040 nonbonded pdb=" ND2 ASN A 44 " pdb=" OD2 ASP A 72 " model vdw 2.505 3.120 nonbonded pdb=" N HIS A 178 " pdb=" O HIS A 178 " model vdw 2.636 2.496 nonbonded pdb=" O THR A 139 " pdb=" C ASN A 140 " model vdw 2.637 3.270 nonbonded pdb=" N LEU A 57 " pdb=" N HIS A 58 " model vdw 2.644 2.560 ... (remaining 11355 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.460 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.004 0.056 1635 Z= 0.253 Angle : 0.706 7.581 2263 Z= 0.417 Chirality : 0.049 0.200 287 Planarity : 0.007 0.059 298 Dihedral : 10.064 45.872 443 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.56), residues: 248 helix: 2.46 (0.39), residues: 189 sheet: None (None), residues: 0 loop : -1.27 (0.80), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 183 PHE 0.004 0.001 PHE A 161 TYR 0.008 0.001 TYR A 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.239 Fit side-chains REVERT: A 283 LEU cc_start: 0.8388 (tp) cc_final: 0.8146 (tt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0599 time to fit residues: 2.3683 Evaluate side-chains 20 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 15 optimal weight: 0.0060 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.5534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.148922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.135910 restraints weight = 3549.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.137424 restraints weight = 2233.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.138352 restraints weight = 1680.390| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1635 Z= 0.177 Angle : 0.498 4.984 2263 Z= 0.259 Chirality : 0.042 0.123 287 Planarity : 0.006 0.050 298 Dihedral : 3.086 11.212 263 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.11 % Allowed : 17.78 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.56), residues: 248 helix: 2.99 (0.38), residues: 194 sheet: None (None), residues: 0 loop : -0.92 (0.89), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.002 0.001 HIS A 246 PHE 0.011 0.001 PHE A 64 TYR 0.009 0.001 TYR A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.175 Fit side-chains REVERT: A 283 LEU cc_start: 0.8910 (tp) cc_final: 0.8585 (tt) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.0395 time to fit residues: 1.5623 Evaluate side-chains 23 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.0370 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.145669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.132427 restraints weight = 3493.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.133859 restraints weight = 2178.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.134992 restraints weight = 1664.982| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1635 Z= 0.190 Angle : 0.495 5.037 2263 Z= 0.254 Chirality : 0.042 0.123 287 Planarity : 0.005 0.050 298 Dihedral : 3.017 11.268 263 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.11 % Allowed : 16.67 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.56), residues: 248 helix: 3.25 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -1.10 (0.85), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.002 0.001 HIS A 107 PHE 0.007 0.001 PHE A 64 TYR 0.011 0.001 TYR A 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.161 Fit side-chains REVERT: A 283 LEU cc_start: 0.8884 (tp) cc_final: 0.8545 (tt) outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0400 time to fit residues: 1.3764 Evaluate side-chains 21 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.0040 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.145495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.132007 restraints weight = 3498.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.133587 restraints weight = 2183.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.134695 restraints weight = 1622.102| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1635 Z= 0.175 Angle : 0.486 5.039 2263 Z= 0.246 Chirality : 0.042 0.123 287 Planarity : 0.005 0.048 298 Dihedral : 2.919 11.480 263 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.22 % Allowed : 15.56 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.56), residues: 248 helix: 3.35 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -1.21 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.004 0.001 HIS A 246 PHE 0.006 0.001 PHE A 64 TYR 0.010 0.001 TYR A 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.169 Fit side-chains REVERT: A 283 LEU cc_start: 0.8846 (tp) cc_final: 0.8526 (tt) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.0425 time to fit residues: 1.5411 Evaluate side-chains 23 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.0000 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.143675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.130030 restraints weight = 3537.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.131660 restraints weight = 2203.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.132819 restraints weight = 1624.849| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1635 Z= 0.191 Angle : 0.499 5.076 2263 Z= 0.252 Chirality : 0.042 0.123 287 Planarity : 0.005 0.047 298 Dihedral : 2.966 11.330 263 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.22 % Allowed : 16.67 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.56), residues: 248 helix: 3.40 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.23 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 246 PHE 0.005 0.001 PHE A 161 TYR 0.011 0.001 TYR A 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.179 Fit side-chains REVERT: A 283 LEU cc_start: 0.8861 (tp) cc_final: 0.8521 (tt) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.0422 time to fit residues: 1.5578 Evaluate side-chains 24 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.142582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129012 restraints weight = 3582.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.130643 restraints weight = 2271.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.131750 restraints weight = 1669.611| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1635 Z= 0.223 Angle : 0.525 5.182 2263 Z= 0.267 Chirality : 0.043 0.124 287 Planarity : 0.005 0.046 298 Dihedral : 3.130 12.660 263 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.56 % Allowed : 13.33 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.56), residues: 248 helix: 3.28 (0.38), residues: 194 sheet: None (None), residues: 0 loop : -1.31 (0.84), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.004 0.001 HIS A 246 PHE 0.006 0.001 PHE A 161 TYR 0.014 0.001 TYR A 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.184 Fit side-chains REVERT: A 283 LEU cc_start: 0.8908 (tp) cc_final: 0.8577 (tt) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.0451 time to fit residues: 1.7490 Evaluate side-chains 25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.0030 overall best weight: 0.4248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.146193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132829 restraints weight = 3515.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.134216 restraints weight = 2200.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.135405 restraints weight = 1663.006| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1635 Z= 0.159 Angle : 0.489 5.623 2263 Z= 0.243 Chirality : 0.041 0.123 287 Planarity : 0.005 0.046 298 Dihedral : 2.886 10.924 263 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.33 % Allowed : 16.67 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.56), residues: 248 helix: 3.47 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.18 (0.86), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.002 0.001 HIS A 246 PHE 0.003 0.000 PHE A 64 TYR 0.007 0.001 TYR A 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.183 Fit side-chains REVERT: A 283 LEU cc_start: 0.8834 (tp) cc_final: 0.8503 (tt) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.0445 time to fit residues: 1.8391 Evaluate side-chains 25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.144453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.130917 restraints weight = 3487.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.132641 restraints weight = 2144.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.133680 restraints weight = 1573.619| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1635 Z= 0.183 Angle : 0.505 5.798 2263 Z= 0.251 Chirality : 0.042 0.123 287 Planarity : 0.005 0.046 298 Dihedral : 2.935 11.426 263 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.22 % Allowed : 21.11 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.56), residues: 248 helix: 3.44 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.23 (0.86), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.002 0.001 HIS A 107 PHE 0.005 0.001 PHE A 161 TYR 0.009 0.001 TYR A 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.169 Fit side-chains REVERT: A 283 LEU cc_start: 0.8834 (tp) cc_final: 0.8523 (tt) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.0437 time to fit residues: 1.6536 Evaluate side-chains 25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 22 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.146965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.133760 restraints weight = 3611.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.135371 restraints weight = 2295.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.136517 restraints weight = 1699.121| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1635 Z= 0.148 Angle : 0.490 6.727 2263 Z= 0.239 Chirality : 0.041 0.123 287 Planarity : 0.005 0.045 298 Dihedral : 2.785 11.010 263 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.22 % Allowed : 21.11 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.56), residues: 248 helix: 3.52 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -1.06 (0.89), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.001 0.001 HIS A 246 PHE 0.004 0.000 PHE A 64 TYR 0.006 0.001 TYR A 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.179 Fit side-chains REVERT: A 283 LEU cc_start: 0.8835 (tp) cc_final: 0.8508 (tt) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.0424 time to fit residues: 1.6027 Evaluate side-chains 25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.144133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130581 restraints weight = 3563.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.132355 restraints weight = 2161.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133401 restraints weight = 1574.947| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1635 Z= 0.191 Angle : 0.513 6.304 2263 Z= 0.254 Chirality : 0.042 0.124 287 Planarity : 0.005 0.045 298 Dihedral : 2.920 11.532 263 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.22 % Allowed : 21.11 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.56), residues: 248 helix: 3.47 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -1.17 (0.87), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 107 PHE 0.005 0.001 PHE A 161 TYR 0.010 0.001 TYR A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.184 Fit side-chains REVERT: A 283 LEU cc_start: 0.8832 (tp) cc_final: 0.8516 (tt) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.0494 time to fit residues: 1.8207 Evaluate side-chains 25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 0.0020 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.145051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.131478 restraints weight = 3678.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133234 restraints weight = 2192.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.134409 restraints weight = 1597.794| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1635 Z= 0.173 Angle : 0.503 6.561 2263 Z= 0.248 Chirality : 0.042 0.124 287 Planarity : 0.005 0.045 298 Dihedral : 2.872 11.384 263 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.22 % Allowed : 21.11 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.56), residues: 248 helix: 3.51 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -1.13 (0.87), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.002 0.001 HIS A 107 PHE 0.004 0.001 PHE A 161 TYR 0.009 0.001 TYR A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 934.76 seconds wall clock time: 17 minutes 19.68 seconds (1039.68 seconds total)