Starting phenix.real_space_refine on Sun Mar 10 14:36:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/03_2024/8j46_35971_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/03_2024/8j46_35971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/03_2024/8j46_35971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/03_2024/8j46_35971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/03_2024/8j46_35971_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/03_2024/8j46_35971_neut.pdb" } resolution = 3.66 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= 0.010 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 1381 2.51 5 N 383 2.21 5 O 390 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 1101": "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: 2158 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2158 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 14, 'TRANS': 347} Chain breaks: 5 Unresolved non-hydrogen bonds: 733 Unresolved non-hydrogen angles: 931 Unresolved non-hydrogen dihedrals: 601 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 12, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 10, 'GLU:plan': 12, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 340 Time building chain proxies: 1.83, per 1000 atoms: 0.85 Number of scatterers: 2158 At special positions: 0 Unit cell: (60.208, 80.56, 109.392, 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 390 8.00 N 383 7.00 C 1381 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: 0.87 Conformation dependent library (CDL) restraints added in 509.0 milliseconds 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 696 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 87.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 29 through 52 removed outlier: 4.342A pdb=" N PHE A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.556A 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: 4.118A pdb=" N PHE A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.804A 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 1019 removed outlier: 3.634A 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) removed outlier: 3.732A pdb=" N ALA A 996 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 997 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A 998 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A1003 " --> pdb=" O GLN A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1044 removed outlier: 3.567A pdb=" N LYS A1032 " --> pdb=" O ASP A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1081 removed outlier: 3.632A pdb=" N ASP A1066 " --> pdb=" O ARG A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 242 removed outlier: 3.855A pdb=" N ALA A1087 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR A1097 " --> pdb=" O GLN A1093 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN A1103 " --> pdb=" O ASN A1099 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A1110 " --> pdb=" O LEU A1106 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER A1111 " --> pdb=" O GLU A1107 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 237 " --> pdb=" O ARG A1110 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 238 " --> pdb=" O SER A1111 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 239 " --> pdb=" O THR A1112 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 240 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) 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: 3.714A pdb=" N CYS A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.554A 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: 3.586A 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) 216 hydrogen bonds defined for protein. 648 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: 0.62 Time building geometry restraints manager: 0.96 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: 643 1.33 - 1.45: 278 1.45 - 1.57: 1269 1.57 - 1.69: 0 1.69 - 1.80: 4 Bond restraints: 2194 Sorted by residual: bond pdb=" N PRO A 11 " pdb=" CD PRO A 11 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" C MET A 112 " pdb=" O MET A 112 " ideal model delta sigma weight residual 1.237 1.218 0.019 1.19e-02 7.06e+03 2.48e+00 bond pdb=" N HIS A1063 " pdb=" CA HIS A1063 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.21e-02 6.83e+03 2.18e+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 2.13e+00 bond pdb=" C LEU A 156 " pdb=" O LEU A 156 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.17e-02 7.31e+03 2.01e+00 ... (remaining 2189 not shown) Histogram of bond angle deviations from ideal: 102.20 - 108.03: 81 108.03 - 113.86: 1220 113.86 - 119.69: 581 119.69 - 125.52: 1137 125.52 - 131.35: 21 Bond angle restraints: 3040 Sorted by residual: angle pdb=" N ALA A 226 " pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 111.36 117.35 -5.99 1.09e+00 8.42e-01 3.02e+01 angle pdb=" N THR A1112 " pdb=" CA THR A1112 " pdb=" C THR A1112 " ideal model delta sigma weight residual 111.36 117.21 -5.85 1.09e+00 8.42e-01 2.88e+01 angle pdb=" N LEU A 237 " pdb=" CA LEU A 237 " pdb=" C LEU A 237 " ideal model delta sigma weight residual 111.28 116.26 -4.98 1.09e+00 8.42e-01 2.09e+01 angle pdb=" N LYS A1015 " pdb=" CA LYS A1015 " pdb=" C LYS A1015 " ideal model delta sigma weight residual 111.28 106.42 4.86 1.09e+00 8.42e-01 1.99e+01 angle pdb=" N ASN A1022 " pdb=" CA ASN A1022 " pdb=" C ASN A1022 " ideal model delta sigma weight residual 109.24 115.74 -6.50 1.51e+00 4.39e-01 1.86e+01 ... (remaining 3035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.19: 1176 9.19 - 18.37: 51 18.37 - 27.56: 25 27.56 - 36.74: 19 36.74 - 45.93: 4 Dihedral angle restraints: 1275 sinusoidal: 213 harmonic: 1062 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 -118.25 32.25 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 180.00 137.88 42.12 3 1.50e+01 4.44e-03 7.55e+00 dihedral pdb=" N LEU A1038 " pdb=" CA LEU A1038 " pdb=" CB LEU A1038 " pdb=" CG LEU A1038 " ideal model delta sinusoidal sigma weight residual -60.00 -101.23 41.23 3 1.50e+01 4.44e-03 7.37e+00 ... (remaining 1272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 326 0.061 - 0.122: 56 0.122 - 0.183: 9 0.183 - 0.244: 2 0.244 - 0.305: 1 Chirality restraints: 394 Sorted by residual: chirality pdb=" CA TYR A1101 " pdb=" N TYR A1101 " pdb=" C TYR A1101 " pdb=" CB TYR A1101 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ASP A1021 " pdb=" N ASP A1021 " pdb=" C ASP A1021 " pdb=" CB ASP A1021 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 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 9.58e-01 ... (remaining 391 not shown) Planarity restraints: 406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 225 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ARG A 225 " 0.060 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 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+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 5.59e-02 5.00e+00 pdb=" N PRO A 287 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.032 5.00e-02 4.00e+02 ... (remaining 403 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 1006 2.95 - 3.44: 2404 3.44 - 3.93: 3253 3.93 - 4.41: 3225 4.41 - 4.90: 5483 Nonbonded interactions: 15371 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 2.506 2.520 nonbonded pdb=" O ASP A1005 " pdb=" OD1 ASP A1005 " model vdw 2.554 3.040 nonbonded pdb=" O ASN A1013 " pdb=" OD1 ASN A1013 " model vdw 2.563 3.040 nonbonded pdb=" O VAL A1016 " pdb=" O LYS A1019 " model vdw 2.577 3.040 ... (remaining 15366 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: 1.520 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: 6.390 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.760 Find NCS groups from input model: 0.070 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 0.055 2194 Z= 0.258 Angle : 0.772 7.551 3040 Z= 0.525 Chirality : 0.052 0.305 394 Planarity : 0.006 0.059 406 Dihedral : 9.516 45.928 576 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 16.35 % Favored : 83.65 % 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: 2.69 (0.46), residues: 350 helix: 2.46 (0.31), residues: 282 sheet: None (None), residues: 0 loop : -1.28 (0.72), residues: 68 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 ARG 0.001 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.244 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0711 time to fit residues: 5.2054 Evaluate side-chains 30 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN A 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 2194 Z= 0.437 Angle : 0.758 9.088 3040 Z= 0.427 Chirality : 0.046 0.144 394 Planarity : 0.006 0.049 406 Dihedral : 4.275 17.218 367 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.73 % Allowed : 23.08 % Favored : 70.19 % 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: 1.17 (0.44), residues: 350 helix: 1.43 (0.29), residues: 297 sheet: None (None), residues: 0 loop : -2.94 (0.73), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.017 0.004 HIS A 178 PHE 0.025 0.003 PHE A 87 TYR 0.016 0.002 TYR A 62 ARG 0.004 0.002 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.245 Fit side-chains REVERT: A 37 TYR cc_start: 0.9035 (t80) cc_final: 0.8774 (t80) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.0732 time to fit residues: 3.6139 Evaluate side-chains 32 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2194 Z= 0.153 Angle : 0.534 8.191 3040 Z= 0.273 Chirality : 0.040 0.126 394 Planarity : 0.004 0.049 406 Dihedral : 3.281 11.406 367 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 4.81 % Allowed : 21.15 % Favored : 74.04 % 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 (0.47), residues: 350 helix: 2.65 (0.31), residues: 294 sheet: None (None), residues: 0 loop : -2.76 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.006 0.002 HIS A 178 PHE 0.012 0.002 PHE A 87 TYR 0.009 0.001 TYR A 125 ARG 0.002 0.001 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.252 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.0723 time to fit residues: 3.5861 Evaluate side-chains 34 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 1063 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2194 Z= 0.145 Angle : 0.495 6.530 3040 Z= 0.255 Chirality : 0.039 0.144 394 Planarity : 0.004 0.044 406 Dihedral : 3.127 12.052 367 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.88 % Allowed : 25.00 % Favored : 72.12 % 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: 3.31 (0.48), residues: 350 helix: 2.90 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -2.93 (0.74), residues: 48 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 0.037 0.002 PHE A 87 TYR 0.016 0.001 TYR A 37 ARG 0.000 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.272 Fit side-chains REVERT: A 80 ILE cc_start: 0.9397 (mm) cc_final: 0.9127 (tp) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.0762 time to fit residues: 3.9987 Evaluate side-chains 34 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 97 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 31 optimal weight: 0.0870 chunk 8 optimal weight: 0.4980 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2194 Z= 0.217 Angle : 0.523 4.934 3040 Z= 0.279 Chirality : 0.040 0.132 394 Planarity : 0.004 0.042 406 Dihedral : 3.338 11.666 367 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.77 % Allowed : 23.08 % Favored : 71.15 % 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: 3.17 (0.48), residues: 350 helix: 2.79 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -2.79 (0.76), residues: 49 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 0.011 0.001 PHE A 104 TYR 0.014 0.001 TYR A 37 ARG 0.001 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.240 Fit side-chains REVERT: A 37 TYR cc_start: 0.8894 (t80) cc_final: 0.8298 (t80) REVERT: A 80 ILE cc_start: 0.9411 (mm) cc_final: 0.9044 (mt) outliers start: 6 outliers final: 6 residues processed: 36 average time/residue: 0.0717 time to fit residues: 3.5680 Evaluate side-chains 39 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 1063 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.0040 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2194 Z= 0.159 Angle : 0.489 5.308 3040 Z= 0.255 Chirality : 0.039 0.156 394 Planarity : 0.004 0.040 406 Dihedral : 3.197 11.681 367 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.81 % Allowed : 27.88 % Favored : 67.31 % 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: 3.44 (0.48), residues: 350 helix: 2.95 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -2.82 (0.77), residues: 47 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 0.008 0.001 PHE A 87 TYR 0.013 0.001 TYR A 37 ARG 0.000 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.259 Fit side-chains REVERT: A 37 TYR cc_start: 0.8833 (t80) cc_final: 0.8201 (t80) REVERT: A 80 ILE cc_start: 0.9382 (mm) cc_final: 0.8999 (mt) outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.0782 time to fit residues: 3.9942 Evaluate side-chains 39 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 1063 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2194 Z= 0.157 Angle : 0.491 5.005 3040 Z= 0.259 Chirality : 0.039 0.164 394 Planarity : 0.004 0.038 406 Dihedral : 3.138 11.971 367 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 5.77 % Allowed : 27.88 % Favored : 66.35 % 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: 3.52 (0.47), residues: 350 helix: 3.01 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -2.66 (0.77), residues: 48 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 0.053 0.002 PHE A 87 TYR 0.013 0.001 TYR A 37 ARG 0.000 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.225 Fit side-chains REVERT: A 37 TYR cc_start: 0.8841 (t80) cc_final: 0.8379 (t80) REVERT: A 80 ILE cc_start: 0.9348 (mm) cc_final: 0.9102 (tp) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.0636 time to fit residues: 3.4194 Evaluate side-chains 37 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 181 CYS Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 293 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 31 optimal weight: 0.0270 chunk 33 optimal weight: 0.0570 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 overall best weight: 1.0316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2194 Z= 0.150 Angle : 0.482 4.840 3040 Z= 0.253 Chirality : 0.039 0.194 394 Planarity : 0.004 0.040 406 Dihedral : 3.047 10.483 367 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.81 % Allowed : 29.81 % Favored : 65.38 % 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: 3.61 (0.47), residues: 350 helix: 3.06 (0.30), residues: 302 sheet: None (None), residues: 0 loop : -2.57 (0.77), residues: 48 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 0.038 0.002 PHE A 87 TYR 0.012 0.001 TYR A 37 ARG 0.001 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.254 Fit side-chains REVERT: A 37 TYR cc_start: 0.8837 (t80) cc_final: 0.8369 (t80) REVERT: A 80 ILE cc_start: 0.9309 (mm) cc_final: 0.9007 (tp) outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.0715 time to fit residues: 3.6475 Evaluate side-chains 39 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 181 CYS Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 293 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.0970 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.4320 ------------------------------------------------------------------------------- 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: 0.7528 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2194 Z= 0.167 Angle : 0.490 4.984 3040 Z= 0.260 Chirality : 0.040 0.183 394 Planarity : 0.004 0.040 406 Dihedral : 3.098 10.353 367 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.85 % Allowed : 29.81 % Favored : 66.35 % 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: 3.50 (0.47), residues: 350 helix: 3.00 (0.30), residues: 302 sheet: None (None), residues: 0 loop : -2.70 (0.76), residues: 48 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 0.012 0.001 PHE A 87 TYR 0.012 0.001 TYR A 37 ARG 0.001 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.239 Fit side-chains REVERT: A 37 TYR cc_start: 0.8858 (t80) cc_final: 0.8574 (t80) outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.0691 time to fit residues: 3.5035 Evaluate side-chains 37 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 1063 HIS Chi-restraints excluded: chain A residue 293 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1006 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2194 Z= 0.278 Angle : 0.577 6.177 3040 Z= 0.315 Chirality : 0.042 0.197 394 Planarity : 0.004 0.039 406 Dihedral : 3.519 11.556 367 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.85 % Allowed : 31.73 % Favored : 64.42 % 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: 2.98 (0.46), residues: 350 helix: 2.65 (0.30), residues: 295 sheet: -0.79 (2.94), residues: 4 loop : -2.22 (0.86), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.008 0.002 HIS A 107 PHE 0.014 0.002 PHE A 104 TYR 0.014 0.002 TYR A 37 ARG 0.002 0.001 ARG A 997 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.252 Fit side-chains REVERT: A 37 TYR cc_start: 0.8906 (t80) cc_final: 0.8630 (t80) outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.0680 time to fit residues: 3.3773 Evaluate side-chains 36 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 1063 HIS Chi-restraints excluded: chain A residue 293 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.0170 chunk 1 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.077204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067388 restraints weight = 14047.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.068560 restraints weight = 9347.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.069281 restraints weight = 6951.839| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2194 Z= 0.145 Angle : 0.490 5.527 3040 Z= 0.256 Chirality : 0.039 0.181 394 Planarity : 0.004 0.043 406 Dihedral : 3.104 11.187 367 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.88 % Allowed : 31.73 % Favored : 65.38 % 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 (0.47), residues: 350 helix: 3.04 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -2.13 (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 0.013 0.001 PHE A 87 TYR 0.013 0.001 TYR A 37 ARG 0.000 0.000 ARG A 997 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 790.28 seconds wall clock time: 14 minutes 43.03 seconds (883.03 seconds total)