Starting phenix.real_space_refine on Wed Mar 5 15:14:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j46_35971/03_2025/8j46_35971_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j46_35971/03_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_35971/03_2025/8j46_35971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j46_35971/03_2025/8j46_35971.map" model { file = "/net/cci-nas-00/data/ceres_data/8j46_35971/03_2025/8j46_35971_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j46_35971/03_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-5624/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: 2.71, per 1000 atoms: 1.26 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: 0.58 Conformation dependent library (CDL) restraints added in 375.5 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: 0.64 Time building geometry restraints manager: 0.69 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: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.080 Find NCS groups from input model: 0.030 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- 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 : 0.239 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0739 time to fit residues: 5.4030 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 : 0.238 ------------------------------------------------------------------------------- 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 = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065015 restraints weight = 9791.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.065798 restraints weight = 7511.218| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.250 Fit side-chains REVERT: A 37 TYR cc_start: 0.8957 (t80) cc_final: 0.8649 (t80) outliers start: 4 outliers final: 1 residues processed: 34 average time/residue: 0.0738 time to fit residues: 3.4814 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: 0.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A1006 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.076293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.066388 restraints weight = 14020.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.067480 restraints weight = 9431.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.068300 restraints weight = 7130.416| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2194 Z= 0.172 Angle : 0.537 7.763 3040 Z= 0.274 Chirality : 0.040 0.127 394 Planarity : 0.004 0.046 406 Dihedral : 3.238 11.122 367 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 5.77 % Allowed : 22.12 % 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: 2.91 (0.47), residues: 350 helix: 2.63 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -2.65 (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 0.010 0.002 PHE A 87 TYR 0.008 0.001 TYR A 125 ARG 0.001 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 39 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.240 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 0.0740 time to fit residues: 3.7313 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 : 0.254 ------------------------------------------------------------------------------- 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: 0.1980 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.076238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.066453 restraints weight = 13718.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.067516 restraints weight = 9215.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.068295 restraints weight = 7053.881| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3270 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= 0.171 Angle : 0.513 5.490 3040 Z= 0.266 Chirality : 0.039 0.139 394 Planarity : 0.004 0.043 406 Dihedral : 3.174 11.865 367 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.77 % Allowed : 22.12 % 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: 3.14 (0.48), residues: 350 helix: 2.77 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -2.90 (0.75), 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 0.036 0.002 PHE A 87 TYR 0.013 0.001 TYR A 37 ARG 0.001 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 41 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.215 Fit side-chains REVERT: A 37 TYR cc_start: 0.8880 (t80) cc_final: 0.8659 (t80) REVERT: A 80 ILE cc_start: 0.9407 (mm) cc_final: 0.9125 (mt) outliers start: 6 outliers final: 3 residues processed: 38 average time/residue: 0.0692 time to fit residues: 3.6620 Evaluate side-chains 35 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 1063 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 0.0060 overall best weight: 1.5800 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.076494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.066355 restraints weight = 14011.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.067582 restraints weight = 9248.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.068305 restraints weight = 6911.917| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3572 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 : 0.502 4.937 3040 Z= 0.265 Chirality : 0.040 0.143 394 Planarity : 0.004 0.040 406 Dihedral : 3.196 12.269 367 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.81 % Allowed : 25.96 % Favored : 69.23 % 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: 3.28 (0.48), residues: 350 helix: 2.86 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -3.00 (0.76), residues: 47 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 0.009 0.001 PHE A 87 TYR 0.008 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 to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.187 Fit side-chains REVERT: A 37 TYR cc_start: 0.8812 (t80) cc_final: 0.8556 (t80) REVERT: A 80 ILE cc_start: 0.9357 (mm) cc_final: 0.9029 (mt) outliers start: 5 outliers final: 2 residues processed: 37 average time/residue: 0.0727 time to fit residues: 3.7582 Evaluate side-chains 37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE 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: 3.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.0470 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.074256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064184 restraints weight = 14438.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.065282 restraints weight = 9700.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065981 restraints weight = 7338.011| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2194 Z= 0.277 Angle : 0.586 6.201 3040 Z= 0.318 Chirality : 0.042 0.144 394 Planarity : 0.004 0.041 406 Dihedral : 3.685 15.787 367 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.85 % Allowed : 25.96 % 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: 2.79 (0.47), residues: 350 helix: 2.52 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -2.81 (0.77), residues: 49 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 0.045 0.003 PHE A 87 TYR 0.005 0.001 TYR A 134 ARG 0.001 0.001 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: 4 poor density : 36 time to evaluate : 0.243 Fit side-chains REVERT: A 14 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: A 80 ILE cc_start: 0.9369 (mm) cc_final: 0.9113 (tp) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.0703 time to fit residues: 3.7949 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 : 0.254 ------------------------------------------------------------------------------- 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 1063 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 0.0670 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.076693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066665 restraints weight = 14023.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067894 restraints weight = 9106.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.068721 restraints weight = 6716.338| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2194 Z= 0.163 Angle : 0.516 6.205 3040 Z= 0.276 Chirality : 0.040 0.174 394 Planarity : 0.004 0.041 406 Dihedral : 3.216 11.842 367 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.81 % Allowed : 26.92 % Favored : 68.27 % 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: 3.38 (0.48), residues: 350 helix: 2.95 (0.31), residues: 295 sheet: None (None), residues: 0 loop : -2.19 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.002 0.001 HIS A 107 PHE 0.013 0.001 PHE A 87 TYR 0.017 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 42 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8844 (t80) cc_final: 0.8419 (t80) REVERT: A 80 ILE cc_start: 0.9375 (mm) cc_final: 0.9137 (tp) outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 0.0767 time to fit residues: 4.2887 Evaluate side-chains 37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 181 CYS 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: 6.9990 chunk 21 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.074162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.064277 restraints weight = 14436.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.065346 restraints weight = 9693.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.066153 restraints weight = 7205.656| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4364 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= 0.250 Angle : 0.556 5.536 3040 Z= 0.302 Chirality : 0.042 0.199 394 Planarity : 0.004 0.040 406 Dihedral : 3.441 11.530 367 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.81 % Allowed : 28.85 % 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: 3.06 (0.47), residues: 350 helix: 2.68 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -2.02 (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 0.017 0.002 PHE A 87 TYR 0.009 0.002 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 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 14 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: A 37 TYR cc_start: 0.8831 (t80) cc_final: 0.8269 (t80) REVERT: A 80 ILE cc_start: 0.9369 (mm) cc_final: 0.8992 (mt) REVERT: A 99 CYS cc_start: 0.6820 (m) cc_final: 0.6427 (m) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.0699 time to fit residues: 3.5975 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 : 0.232 ------------------------------------------------------------------------------- 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 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: 0.0000 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 overall best weight: 1.2088 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.075716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.065832 restraints weight = 13938.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066973 restraints weight = 9013.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.067818 restraints weight = 6685.968| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4397 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= 0.165 Angle : 0.501 4.974 3040 Z= 0.265 Chirality : 0.040 0.189 394 Planarity : 0.004 0.040 406 Dihedral : 3.195 11.411 367 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.88 % Allowed : 29.81 % 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: 3.46 (0.47), residues: 350 helix: 2.95 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -1.91 (0.87), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 246 PHE 0.017 0.001 PHE A 87 TYR 0.010 0.001 TYR A 37 ARG 0.000 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 37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.219 Fit side-chains REVERT: A 37 TYR cc_start: 0.8679 (t80) cc_final: 0.8155 (t80) REVERT: A 80 ILE cc_start: 0.9320 (mm) cc_final: 0.8955 (mt) REVERT: A 99 CYS cc_start: 0.6595 (m) cc_final: 0.6156 (m) outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.0672 time to fit residues: 3.3756 Evaluate side-chains 36 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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: 0.0270 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.0050 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5652 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.077210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.067237 restraints weight = 13705.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.068334 restraints weight = 9130.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.069024 restraints weight = 6876.487| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4500 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= 0.143 Angle : 0.490 5.343 3040 Z= 0.254 Chirality : 0.039 0.181 394 Planarity : 0.004 0.040 406 Dihedral : 3.035 11.233 367 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.92 % Allowed : 31.73 % 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: 3.64 (0.47), residues: 350 helix: 3.01 (0.30), residues: 304 sheet: None (None), residues: 0 loop : -2.29 (0.82), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.006 0.001 HIS A 246 PHE 0.017 0.001 PHE A 87 TYR 0.011 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 36 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.228 Fit side-chains REVERT: A 37 TYR cc_start: 0.8628 (t80) cc_final: 0.8198 (t80) REVERT: A 80 ILE cc_start: 0.9276 (mm) cc_final: 0.8934 (mt) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.0687 time to fit residues: 3.4757 Evaluate side-chains 34 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 1063 HIS 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: 5.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 30 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.074465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064647 restraints weight = 14295.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065718 restraints weight = 9485.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.066521 restraints weight = 7143.049| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2194 Z= 0.274 Angle : 0.569 5.341 3040 Z= 0.309 Chirality : 0.042 0.168 394 Planarity : 0.004 0.040 406 Dihedral : 3.343 10.695 367 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 3.23 (0.47), residues: 350 helix: 2.80 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -1.96 (0.87), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.008 0.002 HIS A 246 PHE 0.022 0.002 PHE A 253 TYR 0.014 0.002 TYR A 254 ARG 0.001 0.001 ARG A 997 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1071.95 seconds wall clock time: 19 minutes 11.02 seconds (1151.02 seconds total)