Starting phenix.real_space_refine on Fri Aug 22 12:38:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j46_35971/08_2025/8j46_35971_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j46_35971/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j46_35971/08_2025/8j46_35971_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j46_35971/08_2025/8j46_35971_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j46_35971/08_2025/8j46_35971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j46_35971/08_2025/8j46_35971.map" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 12, 'HIS:plan': 5, 'TRP:plan': 3, 'PHE:plan': 10, 'TYR:plan': 5, 'ASN:plan1': 8, 'GLN:plan1': 8, 'ASP:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 340 Time building chain proxies: 1.07, per 1000 atoms: 0.50 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: 0.28 Conformation dependent library (CDL) restraints added in 109.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.04 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: 0.20 Time building geometry restraints manager: 0.29 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.610 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.560 ------------------------------------------------------------------------------- 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 2195 Z= 0.241 Angle : 0.772 7.551 3042 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 997 TYR 0.008 0.001 TYR A 134 PHE 0.004 0.001 PHE A 161 TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2194) covalent geometry : angle 0.77246 ( 3040) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.18290 ( 2) hydrogen bonds : bond 0.17270 ( 216) hydrogen bonds : angle 6.17487 ( 648) *********************** 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 : 0.090 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0320 time to fit residues: 2.3602 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 : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.078712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.068294 restraints weight = 13588.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.069583 restraints weight = 8998.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.070432 restraints weight = 6669.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.071153 restraints weight = 5347.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.071620 restraints weight = 4492.437| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2195 Z= 0.133 Angle : 0.560 5.588 3042 Z= 0.293 Chirality : 0.040 0.119 394 Planarity : 0.005 0.050 406 Dihedral : 3.095 10.868 367 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.92 % Allowed : 25.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.46), residues: 350 helix: 2.65 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -2.26 (0.75), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 997 TYR 0.007 0.001 TYR A 134 PHE 0.034 0.002 PHE A 87 TRP 0.000 0.000 TRP A 28 HIS 0.013 0.003 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 2194) covalent geometry : angle 0.55765 ( 3040) SS BOND : bond 0.00252 ( 1) SS BOND : angle 2.03164 ( 2) hydrogen bonds : bond 0.04410 ( 216) hydrogen bonds : angle 4.13149 ( 648) *********************** 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 34 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.109 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.0314 time to fit residues: 1.5185 Evaluate side-chains 29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 25 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.074234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063929 restraints weight = 14481.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.065109 restraints weight = 9448.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.065966 restraints weight = 7023.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.066493 restraints weight = 5706.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.066543 restraints weight = 4942.927| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2195 Z= 0.234 Angle : 0.615 6.174 3042 Z= 0.337 Chirality : 0.042 0.130 394 Planarity : 0.005 0.042 406 Dihedral : 3.599 15.062 367 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.85 % Allowed : 25.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.46), residues: 350 helix: 2.28 (0.30), residues: 299 sheet: None (None), residues: 0 loop : -2.88 (0.72), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG A 997 TYR 0.013 0.002 TYR A 62 PHE 0.026 0.003 PHE A 87 TRP 0.000 0.000 TRP A 28 HIS 0.007 0.003 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 2194) covalent geometry : angle 0.61295 ( 3040) SS BOND : bond 0.00055 ( 1) SS BOND : angle 1.96535 ( 2) hydrogen bonds : bond 0.05723 ( 216) hydrogen bonds : angle 4.51020 ( 648) *********************** 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 37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.082 Fit side-chains REVERT: A 37 TYR cc_start: 0.8956 (t80) cc_final: 0.8516 (t80) REVERT: A 80 ILE cc_start: 0.9369 (mm) cc_final: 0.9021 (tp) outliers start: 4 outliers final: 1 residues processed: 34 average time/residue: 0.0288 time to fit residues: 1.3845 Evaluate side-chains 31 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.0170 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A1006 ASN A 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.077370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067567 restraints weight = 13940.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.068707 restraints weight = 9229.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.069542 restraints weight = 6957.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.070023 restraints weight = 5670.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.070519 restraints weight = 4963.054| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2195 Z= 0.113 Angle : 0.516 9.350 3042 Z= 0.262 Chirality : 0.040 0.147 394 Planarity : 0.004 0.043 406 Dihedral : 3.117 11.924 367 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.77 % Allowed : 21.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.18 (0.47), residues: 350 helix: 2.78 (0.31), residues: 300 sheet: None (None), residues: 0 loop : -2.50 (0.77), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 997 TYR 0.009 0.001 TYR A 125 PHE 0.012 0.001 PHE A 87 TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 2194) covalent geometry : angle 0.51524 ( 3040) SS BOND : bond 0.00104 ( 1) SS BOND : angle 1.41113 ( 2) hydrogen bonds : bond 0.03990 ( 216) hydrogen bonds : angle 3.63935 ( 648) *********************** 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 43 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.087 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.0309 time to fit residues: 1.6753 Evaluate side-chains 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.083 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 35 optimal weight: 0.0270 chunk 25 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.076687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066499 restraints weight = 13959.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.067692 restraints weight = 9275.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068417 restraints weight = 6926.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.069016 restraints weight = 5717.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.069301 restraints weight = 4946.236| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2195 Z= 0.125 Angle : 0.511 6.029 3042 Z= 0.269 Chirality : 0.039 0.140 394 Planarity : 0.004 0.041 406 Dihedral : 3.114 11.899 367 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.85 % Allowed : 25.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.28 (0.47), residues: 350 helix: 2.85 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -2.75 (0.75), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 997 TYR 0.017 0.001 TYR A 37 PHE 0.056 0.002 PHE A 87 TRP 0.000 0.000 TRP A 28 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 2194) covalent geometry : angle 0.50897 ( 3040) SS BOND : bond 0.00083 ( 1) SS BOND : angle 1.98824 ( 2) hydrogen bonds : bond 0.04027 ( 216) hydrogen bonds : angle 3.73136 ( 648) *********************** 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 41 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.083 Fit side-chains REVERT: A 37 TYR cc_start: 0.8657 (t80) cc_final: 0.8185 (t80) REVERT: A 80 ILE cc_start: 0.9303 (mm) cc_final: 0.8994 (tp) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.0310 time to fit residues: 1.6675 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 : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 0.0270 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3563 r_free = 0.3563 target = 0.073647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063610 restraints weight = 14029.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064614 restraints weight = 9711.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.065318 restraints weight = 7474.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065780 restraints weight = 6195.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066122 restraints weight = 5455.415| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2195 Z= 0.229 Angle : 0.614 5.375 3042 Z= 0.335 Chirality : 0.042 0.152 394 Planarity : 0.004 0.038 406 Dihedral : 3.597 14.481 367 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.47), residues: 350 helix: 2.40 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -2.91 (0.76), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 997 TYR 0.015 0.002 TYR A 37 PHE 0.019 0.002 PHE A 87 TRP 0.000 0.000 TRP A 28 HIS 0.008 0.002 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 2194) covalent geometry : angle 0.60373 ( 3040) SS BOND : bond 0.00846 ( 1) SS BOND : angle 4.29676 ( 2) hydrogen bonds : bond 0.05363 ( 216) hydrogen bonds : angle 4.34553 ( 648) *********************** 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 39 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.090 Fit side-chains REVERT: A 37 TYR cc_start: 0.8704 (t80) cc_final: 0.8302 (t80) REVERT: A 80 ILE cc_start: 0.9324 (mm) cc_final: 0.9027 (tp) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.0334 time to fit residues: 1.7591 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 : 0.080 ------------------------------------------------------------------------------- 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 1063 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 35 optimal weight: 0.0570 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.075640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065474 restraints weight = 14404.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.066580 restraints weight = 9452.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067454 restraints weight = 6994.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.068063 restraints weight = 5630.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.068386 restraints weight = 4822.314| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2195 Z= 0.130 Angle : 0.540 6.975 3042 Z= 0.281 Chirality : 0.039 0.163 394 Planarity : 0.004 0.038 406 Dihedral : 3.288 13.295 367 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.88 % Allowed : 25.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.15 (0.48), residues: 350 helix: 2.74 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -2.54 (0.81), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 997 TYR 0.015 0.001 TYR A 37 PHE 0.014 0.001 PHE A 87 TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2194) covalent geometry : angle 0.51199 ( 3040) SS BOND : bond 0.00986 ( 1) SS BOND : angle 6.68574 ( 2) hydrogen bonds : bond 0.04202 ( 216) hydrogen bonds : angle 3.74838 ( 648) *********************** 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 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.109 Fit side-chains REVERT: A 37 TYR cc_start: 0.8635 (t80) cc_final: 0.8041 (t80) REVERT: A 80 ILE cc_start: 0.9292 (mm) cc_final: 0.8883 (mt) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.0329 time to fit residues: 1.6805 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 : 0.086 ------------------------------------------------------------------------------- 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 1063 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.073943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.063821 restraints weight = 14201.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064904 restraints weight = 9392.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.065702 restraints weight = 7057.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066187 restraints weight = 5734.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066636 restraints weight = 4997.146| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2195 Z= 0.188 Angle : 0.567 5.408 3042 Z= 0.305 Chirality : 0.041 0.178 394 Planarity : 0.004 0.036 406 Dihedral : 3.440 12.143 367 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.88 % Allowed : 24.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.47), residues: 350 helix: 2.50 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -2.56 (0.83), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG A 997 TYR 0.014 0.002 TYR A 37 PHE 0.013 0.001 PHE A 104 TRP 0.000 0.000 TRP A 28 HIS 0.006 0.002 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 2194) covalent geometry : angle 0.56064 ( 3040) SS BOND : bond 0.01036 ( 1) SS BOND : angle 3.39895 ( 2) hydrogen bonds : bond 0.04955 ( 216) hydrogen bonds : angle 4.07626 ( 648) *********************** 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 36 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.087 Fit side-chains REVERT: A 37 TYR cc_start: 0.8739 (t80) cc_final: 0.8170 (t80) REVERT: A 80 ILE cc_start: 0.9302 (mm) cc_final: 0.8894 (mt) outliers start: 3 outliers final: 3 residues processed: 35 average time/residue: 0.0320 time to fit residues: 1.5645 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 : 0.084 ------------------------------------------------------------------------------- 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 1063 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.074767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064763 restraints weight = 14261.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.065889 restraints weight = 9302.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.066692 restraints weight = 6920.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.067257 restraints weight = 5576.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.067720 restraints weight = 4823.611| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2195 Z= 0.131 Angle : 0.509 5.016 3042 Z= 0.268 Chirality : 0.040 0.184 394 Planarity : 0.004 0.039 406 Dihedral : 3.246 11.368 367 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.88 % Allowed : 25.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.18 (0.47), residues: 350 helix: 2.77 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -2.56 (0.82), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 997 TYR 0.013 0.001 TYR A 37 PHE 0.007 0.001 PHE A 104 TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2194) covalent geometry : angle 0.50876 ( 3040) SS BOND : bond 0.00007 ( 1) SS BOND : angle 0.63553 ( 2) hydrogen bonds : bond 0.04301 ( 216) hydrogen bonds : angle 3.74885 ( 648) *********************** 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 39 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.085 Fit side-chains REVERT: A 37 TYR cc_start: 0.8656 (t80) cc_final: 0.8071 (t80) REVERT: A 80 ILE cc_start: 0.9287 (mm) cc_final: 0.8884 (mt) outliers start: 3 outliers final: 3 residues processed: 38 average time/residue: 0.0313 time to fit residues: 1.6446 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 : 0.083 ------------------------------------------------------------------------------- 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 1063 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 8 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.076619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.066675 restraints weight = 14584.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.067856 restraints weight = 9413.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.068710 restraints weight = 6929.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.069384 restraints weight = 5540.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.069775 restraints weight = 4689.573| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2195 Z= 0.109 Angle : 0.491 6.099 3042 Z= 0.254 Chirality : 0.040 0.181 394 Planarity : 0.004 0.040 406 Dihedral : 3.068 11.126 367 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.88 % Allowed : 26.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.62 (0.47), residues: 350 helix: 3.03 (0.30), residues: 303 sheet: None (None), residues: 0 loop : -2.43 (0.79), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 997 TYR 0.011 0.001 TYR A 37 PHE 0.026 0.001 PHE A 87 TRP 0.000 0.000 TRP A 28 HIS 0.002 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 2194) covalent geometry : angle 0.49114 ( 3040) SS BOND : bond 0.00357 ( 1) SS BOND : angle 0.39211 ( 2) hydrogen bonds : bond 0.03526 ( 216) hydrogen bonds : angle 3.43294 ( 648) ********************** 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 39 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.079 Fit side-chains REVERT: A 37 TYR cc_start: 0.8758 (t80) cc_final: 0.8494 (t80) outliers start: 3 outliers final: 3 residues processed: 38 average time/residue: 0.0313 time to fit residues: 1.6765 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 : 0.102 ------------------------------------------------------------------------------- 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 1063 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.077194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067042 restraints weight = 14417.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.068206 restraints weight = 9645.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.068990 restraints weight = 7188.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.069513 restraints weight = 5885.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.070097 restraints weight = 5127.171| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2195 Z= 0.106 Angle : 0.491 5.884 3042 Z= 0.253 Chirality : 0.039 0.176 394 Planarity : 0.004 0.041 406 Dihedral : 3.007 10.712 367 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.88 % Allowed : 24.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.64 (0.47), residues: 350 helix: 3.01 (0.30), residues: 304 sheet: None (None), residues: 0 loop : -2.22 (0.84), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 997 TYR 0.012 0.001 TYR A 220 PHE 0.007 0.001 PHE A 96 TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 2194) covalent geometry : angle 0.49042 ( 3040) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.95733 ( 2) hydrogen bonds : bond 0.03329 ( 216) hydrogen bonds : angle 3.35668 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 697.43 seconds wall clock time: 12 minutes 48.82 seconds (768.82 seconds total)