Starting phenix.real_space_refine on Fri Aug 2 12:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/08_2024/8w77_37336_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/08_2024/8w77_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/08_2024/8w77_37336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/08_2024/8w77_37336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/08_2024/8w77_37336_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/08_2024/8w77_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 Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 2.78, per 1000 atoms: 1.74 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 - 3.50 Amino acid : False - 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: 0.71 Conformation dependent library (CDL) restraints added in 676.4 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: 0.20 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: 0.47 Time building geometry restraints manager: 0.79 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: 102.23 - 108.05: 75 108.05 - 113.87: 900 113.87 - 119.68: 431 119.68 - 125.50: 837 125.50 - 131.32: 20 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: 1.600 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.960 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.188 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: 0.0523 time to fit residues: 2.0413 Evaluate side-chains 20 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.189 Fit side-chains REVERT: A 283 LEU cc_start: 0.8375 (tp) cc_final: 0.8103 (tt) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.0491 time to fit residues: 1.8458 Evaluate side-chains 23 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 6 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1444 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= 0.200 Angle : 0.505 5.048 2263 Z= 0.261 Chirality : 0.042 0.123 287 Planarity : 0.005 0.050 298 Dihedral : 3.072 11.690 263 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: 3.57 (0.56), residues: 248 helix: 3.22 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -1.12 (0.84), residues: 54 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 0.006 0.001 PHE A 64 TYR 0.013 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 23 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.182 Fit side-chains REVERT: A 283 LEU cc_start: 0.8350 (tp) cc_final: 0.8067 (tt) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.0422 time to fit residues: 1.4970 Evaluate side-chains 22 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 1635 Z= 0.339 Angle : 0.590 5.311 2263 Z= 0.312 Chirality : 0.045 0.132 287 Planarity : 0.006 0.048 298 Dihedral : 3.558 14.614 263 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.44 % Allowed : 15.56 % 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: 3.00 (0.55), residues: 248 helix: 2.83 (0.38), residues: 193 sheet: None (None), residues: 0 loop : -1.31 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.005 0.002 HIS A 246 PHE 0.009 0.001 PHE A 161 TYR 0.021 0.002 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 fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.191 Fit side-chains REVERT: A 283 LEU cc_start: 0.8425 (tp) cc_final: 0.8138 (tt) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.0465 time to fit residues: 1.6781 Evaluate side-chains 22 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1891 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= 0.187 Angle : 0.501 5.060 2263 Z= 0.256 Chirality : 0.042 0.124 287 Planarity : 0.005 0.047 298 Dihedral : 3.110 11.506 263 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.51 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: 3.53 (0.56), residues: 248 helix: 3.18 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -1.12 (0.86), 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 0.004 0.001 PHE A 161 TYR 0.009 0.001 TYR A 134 *********************** 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 fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.184 Fit side-chains REVERT: A 283 LEU cc_start: 0.8348 (tp) cc_final: 0.8076 (tt) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.0446 time to fit residues: 1.6061 Evaluate side-chains 23 residues out of total 229 non-(ALA, GLY, PRO) need fitting. 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 0.0970 chunk 11 optimal weight: 0.0870 chunk 10 optimal weight: 0.7980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1964 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= 0.153 Angle : 0.485 5.522 2263 Z= 0.240 Chirality : 0.041 0.123 287 Planarity : 0.005 0.046 298 Dihedral : 2.853 10.716 263 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.22 % Allowed : 17.78 % 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: 3.82 (0.57), residues: 248 helix: 3.40 (0.38), 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 246 PHE 0.004 0.001 PHE A 163 TYR 0.006 0.001 TYR A 134 *********************** 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 fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.199 Fit side-chains REVERT: A 283 LEU cc_start: 0.8270 (tp) cc_final: 0.7999 (tt) outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.0483 time to fit residues: 1.8869 Evaluate side-chains 24 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.0570 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1635 Z= 0.254 Angle : 0.545 5.245 2263 Z= 0.279 Chirality : 0.043 0.125 287 Planarity : 0.005 0.045 298 Dihedral : 3.210 12.831 263 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.33 % Allowed : 17.78 % Favored : 78.89 % 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: 3.40 (0.56), residues: 248 helix: 3.16 (0.38), residues: 194 sheet: None (None), residues: 0 loop : -1.43 (0.83), 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 107 PHE 0.006 0.001 PHE A 161 TYR 0.014 0.002 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 26 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.177 Fit side-chains REVERT: A 283 LEU cc_start: 0.8347 (tp) cc_final: 0.8061 (tt) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.0436 time to fit residues: 1.7051 Evaluate side-chains 24 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2100 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 : 0.511 5.906 2263 Z= 0.256 Chirality : 0.042 0.125 287 Planarity : 0.005 0.045 298 Dihedral : 3.069 11.869 263 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.33 % Allowed : 17.78 % Favored : 78.89 % 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: 3.60 (0.56), residues: 248 helix: 3.26 (0.38), residues: 194 sheet: None (None), residues: 0 loop : -1.22 (0.86), 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 0.005 0.001 PHE A 161 TYR 0.010 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 26 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.168 Fit side-chains REVERT: A 283 LEU cc_start: 0.8336 (tp) cc_final: 0.8048 (tt) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.0456 time to fit residues: 1.7434 Evaluate side-chains 26 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 25 optimal weight: 0.2980 chunk 23 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2150 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 : 0.500 6.784 2263 Z= 0.246 Chirality : 0.041 0.124 287 Planarity : 0.005 0.045 298 Dihedral : 2.885 11.243 263 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 : 3.33 % Allowed : 17.78 % Favored : 78.89 % 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: 3.86 (0.57), residues: 248 helix: 3.41 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.05 (0.90), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.001 0.001 HIS A 275 PHE 0.004 0.001 PHE A 64 TYR 0.007 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 26 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.184 Fit side-chains REVERT: A 283 LEU cc_start: 0.8256 (tp) cc_final: 0.7986 (tt) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.0438 time to fit residues: 1.7058 Evaluate side-chains 26 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 20 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2179 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 : 0.511 6.413 2263 Z= 0.253 Chirality : 0.042 0.123 287 Planarity : 0.005 0.045 298 Dihedral : 2.947 11.280 263 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.33 % Allowed : 17.78 % Favored : 78.89 % 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: 3.37 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -1.13 (0.88), 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 0.010 0.001 TYR A 134 ********************** 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 26 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.270 Fit side-chains REVERT: A 283 LEU cc_start: 0.8306 (tp) cc_final: 0.8035 (tt) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.0451 time to fit residues: 1.7697 Evaluate side-chains 26 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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: 0.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.145476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.131998 restraints weight = 3476.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.133788 restraints weight = 2126.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.134977 restraints weight = 1540.137| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2232 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= 0.157 Angle : 0.497 6.723 2263 Z= 0.244 Chirality : 0.041 0.124 287 Planarity : 0.005 0.045 298 Dihedral : 2.825 11.129 263 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.33 % Allowed : 17.78 % Favored : 78.89 % 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: 3.92 (0.56), residues: 248 helix: 3.45 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -1.00 (0.89), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.001 0.001 HIS A 275 PHE 0.004 0.001 PHE A 64 TYR 0.008 0.001 TYR A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 748.93 seconds wall clock time: 13 minutes 49.87 seconds (829.87 seconds total)