Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/03_2024/8w77_37336_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/03_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_37336/03_2024/8w77_37336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/03_2024/8w77_37336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/03_2024/8w77_37336_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w77_37336/03_2024/8w77_37336_neut.pdb" } 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: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 1.29, per 1000 atoms: 0.81 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: 0.62 Conformation dependent library (CDL) restraints added in 300.4 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: 0.45 Time building geometry restraints manager: 0.66 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 2.520 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.300 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.370 Find NCS groups from input model: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.350 ------------------------------------------------------------------------------- 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 : 0.190 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: 0.0531 time to fit residues: 2.0849 Evaluate side-chains 20 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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: 0.4980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7077 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1635 Z= 0.179 Angle : 0.501 4.984 2263 Z= 0.260 Chirality : 0.042 0.123 287 Planarity : 0.006 0.052 298 Dihedral : 3.115 11.308 263 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 0.72 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 0.003 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 25 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.183 Fit side-chains REVERT: A 283 LEU cc_start: 0.8378 (tp) cc_final: 0.8100 (tt) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.0456 time to fit residues: 1.7134 Evaluate side-chains 23 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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: 0.7980 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7083 moved from start: 0.1391 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= 0.176 Angle : 0.488 4.994 2263 Z= 0.249 Chirality : 0.042 0.123 287 Planarity : 0.005 0.051 298 Dihedral : 2.968 10.856 263 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.11 % Allowed : 15.56 % 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: 3.67 (0.56), residues: 248 helix: 3.29 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -1.08 (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 246 PHE 0.007 0.001 PHE A 64 TYR 0.010 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 21 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.198 Fit side-chains REVERT: A 283 LEU cc_start: 0.8338 (tp) cc_final: 0.8070 (tt) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.0418 time to fit residues: 1.3980 Evaluate side-chains 21 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 23 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.7211 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 1635 Z= 0.384 Angle : 0.614 5.412 2263 Z= 0.328 Chirality : 0.046 0.135 287 Planarity : 0.006 0.051 298 Dihedral : 3.648 15.196 263 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.67 % Allowed : 12.22 % 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: 2.83 (0.55), residues: 248 helix: 2.70 (0.37), residues: 193 sheet: None (None), residues: 0 loop : -1.33 (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 0.023 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: 6 poor density : 18 time to evaluate : 0.188 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 21 average time/residue: 0.0424 time to fit residues: 1.4520 Evaluate side-chains 22 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 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 Chi-restraints excluded: chain A residue 250 ILE 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: 1.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.7153 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1635 Z= 0.212 Angle : 0.514 5.102 2263 Z= 0.265 Chirality : 0.042 0.124 287 Planarity : 0.005 0.050 298 Dihedral : 3.231 12.229 263 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 3.37 (0.56), residues: 248 helix: 3.09 (0.38), residues: 194 sheet: None (None), residues: 0 loop : -1.27 (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 246 PHE 0.006 0.001 PHE A 161 TYR 0.012 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 25 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.186 Fit side-chains REVERT: A 283 LEU cc_start: 0.8380 (tp) cc_final: 0.8096 (tt) outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.0436 time to fit residues: 1.6386 Evaluate side-chains 24 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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: 1.9990 chunk 8 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 10 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.1961 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= 0.193 Angle : 0.506 5.125 2263 Z= 0.255 Chirality : 0.042 0.124 287 Planarity : 0.005 0.050 298 Dihedral : 3.086 11.902 263 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 3.57 (0.56), residues: 248 helix: 3.22 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.21 (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 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 25 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.187 Fit side-chains REVERT: A 283 LEU cc_start: 0.8272 (tp) cc_final: 0.7990 (tt) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.0438 time to fit residues: 1.6566 Evaluate side-chains 25 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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=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: 4.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.7236 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 1635 Z= 0.410 Angle : 0.659 5.558 2263 Z= 0.351 Chirality : 0.047 0.137 287 Planarity : 0.006 0.049 298 Dihedral : 3.915 15.832 263 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.56 % Allowed : 16.67 % Favored : 77.78 % 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: 2.54 (0.54), residues: 248 helix: 2.45 (0.37), residues: 192 sheet: None (None), residues: 0 loop : -1.20 (0.86), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.005 0.002 HIS A 107 PHE 0.010 0.002 PHE A 161 TYR 0.022 0.003 TYR A 130 *********************** 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 25 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.188 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 23 average time/residue: 0.0441 time to fit residues: 1.5996 Evaluate side-chains 24 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 250 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 11 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7159 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1635 Z= 0.192 Angle : 0.518 5.943 2263 Z= 0.264 Chirality : 0.042 0.124 287 Planarity : 0.005 0.049 298 Dihedral : 3.250 11.854 263 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.22 % Allowed : 20.00 % Favored : 77.78 % 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: 3.42 (0.56), residues: 248 helix: 3.11 (0.38), residues: 194 sheet: None (None), residues: 0 loop : -1.15 (0.87), 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 0.010 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 23 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.186 Fit side-chains REVERT: A 283 LEU cc_start: 0.8385 (tp) cc_final: 0.8103 (tt) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.0435 time to fit residues: 1.5880 Evaluate side-chains 23 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.0030 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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: 0.7123 moved from start: 0.2216 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= 0.171 Angle : 0.505 6.730 2263 Z= 0.250 Chirality : 0.042 0.124 287 Planarity : 0.005 0.050 298 Dihedral : 2.986 11.435 263 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.22 % Allowed : 20.00 % Favored : 77.78 % 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: 3.73 (0.57), residues: 248 helix: 3.32 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.10 (0.89), 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 161 TYR 0.010 0.001 TYR A 130 *********************** 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: 2 poor density : 24 time to evaluate : 0.192 Fit side-chains REVERT: A 283 LEU cc_start: 0.8282 (tp) cc_final: 0.8002 (tt) outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.0443 time to fit residues: 1.7547 Evaluate side-chains 24 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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: 0.7980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7137 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1635 Z= 0.182 Angle : 0.509 6.303 2263 Z= 0.253 Chirality : 0.042 0.124 287 Planarity : 0.005 0.050 298 Dihedral : 3.016 11.381 263 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.22 % Allowed : 20.00 % Favored : 77.78 % 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: 3.33 (0.38), 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 24 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.181 Fit side-chains REVERT: A 283 LEU cc_start: 0.8311 (tp) cc_final: 0.8033 (tt) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.0421 time to fit residues: 1.5364 Evaluate side-chains 24 residues out of total 229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.143626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.130168 restraints weight = 3481.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.131747 restraints weight = 2171.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.132916 restraints weight = 1599.303| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1635 Z= 0.179 Angle : 0.506 6.559 2263 Z= 0.251 Chirality : 0.042 0.124 287 Planarity : 0.005 0.050 298 Dihedral : 2.983 11.478 263 Min Nonbonded Distance : 2.402 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: 3.80 (0.57), residues: 248 helix: 3.36 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.06 (0.90), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 763.11 seconds wall clock time: 15 minutes 25.54 seconds (925.54 seconds total)