Starting phenix.real_space_refine on Mon Feb 10 20:19:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j46_35971/02_2025/8j46_35971_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j46_35971/02_2025/8j46_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/cci-nas-00/data/ceres_data/8j46_35971/02_2025/8j46_35971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j46_35971/02_2025/8j46_35971.map" model { file = "/net/cci-nas-00/data/ceres_data/8j46_35971/02_2025/8j46_35971_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j46_35971/02_2025/8j46_35971_neut.cif" } 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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 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: 3.41, per 1000 atoms: 1.58 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 333.9 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: 0.23 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: 0.65 Time building geometry restraints manager: 0.67 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: 0.00 - 1.51: 2902 1.51 - 3.02: 102 3.02 - 4.53: 19 4.53 - 6.04: 14 6.04 - 7.55: 3 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 3.120 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: 0.010 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.235 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0745 time to fit residues: 5.5554 Evaluate side-chains 30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.074085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063967 restraints weight = 14419.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.065065 restraints weight = 9791.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.065764 restraints weight = 7440.220| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 2194 Z= 0.374 Angle : 0.709 7.400 3040 Z= 0.398 Chirality : 0.045 0.132 394 Planarity : 0.005 0.049 406 Dihedral : 3.872 15.560 367 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.85 % Allowed : 23.08 % Favored : 73.08 % 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: 1.67 (0.45), residues: 350 helix: 1.75 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -2.77 (0.73), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.013 0.004 HIS A 178 PHE 0.026 0.003 PHE A 87 TYR 0.014 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 37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.249 Fit side-chains REVERT: A 37 TYR cc_start: 0.8970 (t80) cc_final: 0.8660 (t80) outliers start: 4 outliers final: 1 residues processed: 34 average time/residue: 0.0743 time to fit residues: 3.4943 Evaluate side-chains 30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.076071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066162 restraints weight = 14028.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.067207 restraints weight = 9472.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068009 restraints weight = 7232.251| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2194 Z= 0.172 Angle : 0.540 7.279 3040 Z= 0.277 Chirality : 0.040 0.126 394 Planarity : 0.004 0.048 406 Dihedral : 3.269 11.204 367 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 2.86 (0.46), residues: 350 helix: 2.60 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -2.67 (0.72), residues: 52 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 0.009 0.002 PHE A 87 TYR 0.007 0.001 TYR A 125 ARG 0.001 0.000 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 39 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.207 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 0.0718 time to fit residues: 3.5904 Evaluate side-chains 33 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 99 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.073782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.063899 restraints weight = 14067.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.064924 restraints weight = 9709.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.065656 restraints weight = 7458.129| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2194 Z= 0.268 Angle : 0.578 6.396 3040 Z= 0.312 Chirality : 0.041 0.139 394 Planarity : 0.004 0.041 406 Dihedral : 3.551 13.437 367 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.77 % Allowed : 24.04 % 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: 2.67 (0.47), residues: 350 helix: 2.39 (0.30), residues: 305 sheet: None (None), residues: 0 loop : -2.94 (0.80), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.006 0.002 HIS A 107 PHE 0.030 0.002 PHE A 87 TYR 0.011 0.002 TYR A 37 ARG 0.001 0.001 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 40 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.252 Fit side-chains REVERT: A 37 TYR cc_start: 0.8742 (t80) cc_final: 0.8385 (t80) REVERT: A 80 ILE cc_start: 0.9346 (mm) cc_final: 0.9053 (tp) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.0717 time to fit residues: 3.7494 Evaluate side-chains 36 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 1063 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.0060 overall best weight: 1.5802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.075516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.065474 restraints weight = 14420.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.066660 restraints weight = 9409.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.067426 restraints weight = 6948.977| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2194 Z= 0.173 Angle : 0.511 5.492 3040 Z= 0.267 Chirality : 0.040 0.145 394 Planarity : 0.004 0.041 406 Dihedral : 3.284 12.188 367 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 6.73 % Allowed : 26.92 % 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: 3.08 (0.48), residues: 350 helix: 2.75 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -3.07 (0.75), 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 0.031 0.002 PHE A 87 TYR 0.007 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 43 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.226 Fit side-chains REVERT: A 37 TYR cc_start: 0.8843 (t80) cc_final: 0.8604 (t80) REVERT: A 80 ILE cc_start: 0.9392 (mm) cc_final: 0.9093 (mt) outliers start: 7 outliers final: 5 residues processed: 39 average time/residue: 0.0669 time to fit residues: 3.6391 Evaluate side-chains 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 99 CYS Chi-restraints excluded: chain A residue 116 VAL 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 14 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.1004 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.074805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064889 restraints weight = 14271.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.065989 restraints weight = 9513.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.066753 restraints weight = 7185.510| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2194 Z= 0.215 Angle : 0.530 4.980 3040 Z= 0.281 Chirality : 0.040 0.148 394 Planarity : 0.004 0.039 406 Dihedral : 3.380 11.876 367 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.77 % Allowed : 26.92 % 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: 2.98 (0.47), residues: 350 helix: 2.67 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -2.91 (0.75), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.005 0.001 HIS A 107 PHE 0.011 0.001 PHE A 87 TYR 0.005 0.001 TYR A 134 ARG 0.001 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 to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.254 Fit side-chains REVERT: A 14 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: A 37 TYR cc_start: 0.8843 (t80) cc_final: 0.8574 (t80) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.0714 time to fit residues: 3.7678 Evaluate side-chains 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 116 VAL 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 31 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.0030 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.076383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.066389 restraints weight = 14241.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067551 restraints weight = 9232.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.068389 restraints weight = 6848.191| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3958 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= 0.153 Angle : 0.503 5.296 3040 Z= 0.262 Chirality : 0.039 0.159 394 Planarity : 0.004 0.039 406 Dihedral : 3.291 15.110 367 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 3.37 (0.48), residues: 350 helix: 2.94 (0.31), residues: 297 sheet: None (None), residues: 0 loop : -2.35 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 107 PHE 0.008 0.001 PHE A 87 TYR 0.005 0.001 TYR A 134 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 39 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.232 Fit side-chains REVERT: A 37 TYR cc_start: 0.8839 (t80) cc_final: 0.8598 (t80) REVERT: A 80 ILE cc_start: 0.9314 (mm) cc_final: 0.9041 (mt) outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 0.0700 time to fit residues: 3.7102 Evaluate side-chains 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 116 VAL Chi-restraints excluded: chain A residue 1063 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 0.0040 chunk 21 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 overall best weight: 2.3998 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.074916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.064761 restraints weight = 14424.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.065957 restraints weight = 9388.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.066801 restraints weight = 6955.131| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2194 Z= 0.229 Angle : 0.554 5.183 3040 Z= 0.302 Chirality : 0.041 0.191 394 Planarity : 0.004 0.038 406 Dihedral : 3.371 11.507 367 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 6.73 % Allowed : 26.92 % 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: 3.17 (0.48), residues: 350 helix: 2.79 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -2.19 (0.88), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.006 0.002 HIS A 107 PHE 0.019 0.002 PHE A 87 TYR 0.008 0.001 TYR A 220 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 43 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 14 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: A 37 TYR cc_start: 0.8896 (t80) cc_final: 0.8601 (t80) outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.0726 time to fit residues: 4.0023 Evaluate side-chains 43 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 116 VAL 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 32 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.076042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.065918 restraints weight = 13944.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.067106 restraints weight = 9157.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.067987 restraints weight = 6788.669| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2194 Z= 0.185 Angle : 0.522 5.380 3040 Z= 0.281 Chirality : 0.040 0.194 394 Planarity : 0.004 0.042 406 Dihedral : 3.226 13.506 367 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.77 % Allowed : 29.81 % 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: 3.35 (0.47), residues: 350 helix: 2.94 (0.31), residues: 295 sheet: None (None), residues: 0 loop : -2.23 (0.84), residues: 55 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 0.029 0.002 PHE A 87 TYR 0.006 0.001 TYR A 220 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 41 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.229 Fit side-chains REVERT: A 14 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7948 (m-80) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.0711 time to fit residues: 3.8278 Evaluate side-chains 37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 116 VAL 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 33 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.077088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.066980 restraints weight = 13797.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.068193 restraints weight = 9072.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069091 restraints weight = 6752.621| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4577 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= 0.147 Angle : 0.501 5.420 3040 Z= 0.261 Chirality : 0.039 0.185 394 Planarity : 0.004 0.041 406 Dihedral : 3.067 12.680 367 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.85 % Allowed : 30.77 % 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: 3.55 (0.47), residues: 350 helix: 3.03 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -1.99 (0.86), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 107 PHE 0.031 0.002 PHE A 87 TYR 0.019 0.001 TYR A 37 ARG 0.000 0.000 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 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.250 Fit side-chains REVERT: A 37 TYR cc_start: 0.8707 (t80) cc_final: 0.8503 (t80) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.0708 time to fit residues: 3.6569 Evaluate side-chains 37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 116 VAL 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 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.077346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.067147 restraints weight = 13957.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.068275 restraints weight = 9388.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069119 restraints weight = 7102.336| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4681 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= 0.147 Angle : 0.491 5.303 3040 Z= 0.257 Chirality : 0.039 0.179 394 Planarity : 0.004 0.043 406 Dihedral : 2.986 12.161 367 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 3.63 (0.47), residues: 350 helix: 3.03 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -1.69 (0.88), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 246 PHE 0.020 0.001 PHE A 87 TYR 0.015 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: 1065.23 seconds wall clock time: 19 minutes 29.84 seconds (1169.84 seconds total)