Starting phenix.real_space_refine on Wed Jul 23 21:15:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dke_27488/07_2025/8dke_27488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dke_27488/07_2025/8dke_27488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dke_27488/07_2025/8dke_27488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dke_27488/07_2025/8dke_27488.map" model { file = "/net/cci-nas-00/data/ceres_data/8dke_27488/07_2025/8dke_27488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dke_27488/07_2025/8dke_27488.cif" } resolution = 3.18 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= 0.004 sd= 0.089 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 15 5.16 5 C 2861 2.51 5 N 704 2.21 5 O 789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4369 Number of models: 1 Model: "" Number of chains: 3 Chain: "P" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2679 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 3.59, per 1000 atoms: 0.82 Number of scatterers: 4369 At special positions: 0 Unit cell: (83.358, 63.992, 120.406, 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 15 16.00 O 789 8.00 N 704 7.00 C 2861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 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: 1.09 Conformation dependent library (CDL) restraints added in 506.3 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 38.0% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'P' and resid 120 through 140 removed outlier: 3.807A pdb=" N SER P 124 " --> pdb=" O SER P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 153 removed outlier: 4.413A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL P 146 " --> pdb=" O PHE P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 182 removed outlier: 3.572A pdb=" N VAL P 163 " --> pdb=" O SER P 159 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR P 168 " --> pdb=" O ALA P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 removed outlier: 3.553A pdb=" N VAL P 206 " --> pdb=" O ASN P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 258 removed outlier: 3.584A pdb=" N ILE P 238 " --> pdb=" O SER P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 291 removed outlier: 4.104A pdb=" N LYS P 273 " --> pdb=" O PHE P 269 " (cutoff:3.500A) Proline residue: P 283 - end of helix removed outlier: 3.608A pdb=" N PHE P 289 " --> pdb=" O ALA P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 323 removed outlier: 4.212A pdb=" N LEU P 303 " --> pdb=" O ILE P 299 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE P 311 " --> pdb=" O THR P 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET P 316 " --> pdb=" O SER P 312 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN P 323 " --> pdb=" O GLN P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 337 through 357 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.915A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.542A pdb=" N THR A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.172A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'P' and resid 31 through 35 removed outlier: 6.525A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 39 through 43 removed outlier: 3.783A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.521A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 6 removed outlier: 12.307A pdb=" N CYS B 23 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N ALA B 74 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N ALA B 25 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 11.417A pdb=" N THR B 72 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N GLN B 27 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASP B 70 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.492A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.526A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 603 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: 1.10 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1171 1.33 - 1.45: 941 1.45 - 1.58: 2355 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 4489 Sorted by residual: bond pdb=" N TRP P 138 " pdb=" CA TRP P 138 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.22e-02 6.72e+03 1.00e+01 bond pdb=" N GLU A 42 " pdb=" CA GLU A 42 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 7.98e+00 bond pdb=" N VAL P 136 " pdb=" CA VAL P 136 " ideal model delta sigma weight residual 1.461 1.491 -0.031 1.19e-02 7.06e+03 6.70e+00 bond pdb=" N TYR P 134 " pdb=" CA TYR P 134 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.75e+00 bond pdb=" C TRP P 138 " pdb=" O TRP P 138 " ideal model delta sigma weight residual 1.236 1.264 -0.028 1.38e-02 5.25e+03 4.09e+00 ... (remaining 4484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 6100 4.34 - 8.69: 20 8.69 - 13.03: 0 13.03 - 17.37: 0 17.37 - 21.72: 2 Bond angle restraints: 6122 Sorted by residual: angle pdb=" N GLU A 42 " pdb=" CA GLU A 42 " pdb=" C GLU A 42 " ideal model delta sigma weight residual 110.50 88.78 21.72 1.41e+00 5.03e-01 2.37e+02 angle pdb=" C GLU A 42 " pdb=" CA GLU A 42 " pdb=" CB GLU A 42 " ideal model delta sigma weight residual 109.54 127.61 -18.07 1.84e+00 2.95e-01 9.65e+01 angle pdb=" C ALA P 137 " pdb=" N TRP P 138 " pdb=" CA TRP P 138 " ideal model delta sigma weight residual 122.60 114.80 7.80 1.56e+00 4.11e-01 2.50e+01 angle pdb=" C PRO A 62 " pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CA GLU A 42 " pdb=" C GLU A 42 " pdb=" O GLU A 42 " ideal model delta sigma weight residual 121.56 117.26 4.30 1.09e+00 8.42e-01 1.55e+01 ... (remaining 6117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 2274 16.83 - 33.66: 250 33.66 - 50.49: 44 50.49 - 67.32: 9 67.32 - 84.15: 4 Dihedral angle restraints: 2581 sinusoidal: 984 harmonic: 1597 Sorted by residual: dihedral pdb=" C TRP P 138 " pdb=" N TRP P 138 " pdb=" CA TRP P 138 " pdb=" CB TRP P 138 " ideal model delta harmonic sigma weight residual -122.60 -136.74 14.14 0 2.50e+00 1.60e-01 3.20e+01 dihedral pdb=" N TRP P 138 " pdb=" C TRP P 138 " pdb=" CA TRP P 138 " pdb=" CB TRP P 138 " ideal model delta harmonic sigma weight residual 122.80 135.65 -12.85 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 56.54 36.46 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 2578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 659 0.098 - 0.195: 32 0.195 - 0.293: 1 0.293 - 0.390: 0 0.390 - 0.488: 1 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA TRP P 138 " pdb=" N TRP P 138 " pdb=" C TRP P 138 " pdb=" CB TRP P 138 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CA LYS A 43 " pdb=" N LYS A 43 " pdb=" C LYS A 43 " pdb=" CB LYS A 43 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TYR P 134 " pdb=" N TYR P 134 " pdb=" C TYR P 134 " pdb=" CB TYR P 134 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 690 not shown) Planarity restraints: 765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE P 282 " 0.075 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO P 283 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO P 283 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO P 283 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE P 135 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C PHE P 135 " -0.059 2.00e-02 2.50e+03 pdb=" O PHE P 135 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL P 136 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 62 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C PRO A 62 " 0.039 2.00e-02 2.50e+03 pdb=" O PRO A 62 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 63 " -0.013 2.00e-02 2.50e+03 ... (remaining 762 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 230 2.72 - 3.27: 4263 3.27 - 3.81: 6874 3.81 - 4.36: 8155 4.36 - 4.90: 14556 Nonbonded interactions: 34078 Sorted by model distance: nonbonded pdb=" N GLU A 42 " pdb=" O GLU A 42 " model vdw 2.179 2.496 nonbonded pdb=" OG SER P 320 " pdb=" O GLN P 325 " model vdw 2.244 3.040 nonbonded pdb=" O SER A 52 " pdb=" NH1 ARG A 73 " model vdw 2.278 3.120 nonbonded pdb=" O THR A 40 " pdb=" O GLU A 42 " model vdw 2.313 3.040 nonbonded pdb=" O PRO P 49 " pdb=" OH TYR A 100 " model vdw 2.316 3.040 ... (remaining 34073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic 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: 1.840 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.003 0.039 4491 Z= 0.173 Angle : 0.744 21.719 6126 Z= 0.438 Chirality : 0.048 0.488 693 Planarity : 0.006 0.111 765 Dihedral : 14.404 84.146 1555 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.83 % Allowed : 6.02 % Favored : 93.15 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 4.17 % 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: -0.95 (0.37), residues: 547 helix: 1.06 (0.38), residues: 197 sheet: -0.89 (0.44), residues: 156 loop : -2.13 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 132 HIS 0.003 0.001 HIS B 55 PHE 0.035 0.001 PHE P 269 TYR 0.025 0.001 TYR P 173 ARG 0.009 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.15974 ( 215) hydrogen bonds : angle 7.62770 ( 603) SS BOND : bond 0.00305 ( 2) SS BOND : angle 1.61714 ( 4) covalent geometry : bond 0.00324 ( 4489) covalent geometry : angle 0.74328 ( 6122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.488 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 148 MET cc_start: 0.8371 (ttp) cc_final: 0.8105 (tmm) REVERT: A 42 GLU cc_start: 0.5356 (OUTLIER) cc_final: 0.5150 (pp20) REVERT: A 83 GLN cc_start: 0.8384 (tp40) cc_final: 0.8163 (tp40) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.1570 time to fit residues: 11.9647 Evaluate side-chains 55 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain A residue 42 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.135082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.100386 restraints weight = 5305.953| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.19 r_work: 0.2891 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4491 Z= 0.129 Angle : 0.578 7.100 6126 Z= 0.303 Chirality : 0.043 0.174 693 Planarity : 0.004 0.075 765 Dihedral : 5.996 58.629 603 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.24 % Allowed : 9.75 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.63 (0.36), residues: 547 helix: 1.44 (0.38), residues: 194 sheet: -0.70 (0.46), residues: 138 loop : -1.98 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 PHE 0.024 0.001 PHE P 269 TYR 0.019 0.001 TYR P 173 ARG 0.006 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 215) hydrogen bonds : angle 5.33251 ( 603) SS BOND : bond 0.00371 ( 2) SS BOND : angle 1.22817 ( 4) covalent geometry : bond 0.00286 ( 4489) covalent geometry : angle 0.57724 ( 6122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.462 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.5813 (t80) REVERT: P 140 ILE cc_start: 0.8155 (tp) cc_final: 0.7780 (tt) REVERT: P 148 MET cc_start: 0.8456 (ttp) cc_final: 0.7982 (tmm) REVERT: B 81 GLU cc_start: 0.8037 (mp0) cc_final: 0.7791 (mp0) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1625 time to fit residues: 14.4039 Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain A residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.0670 chunk 40 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.133147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.098197 restraints weight = 5287.531| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.19 r_work: 0.2888 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4491 Z= 0.139 Angle : 0.561 6.737 6126 Z= 0.293 Chirality : 0.043 0.172 693 Planarity : 0.004 0.063 765 Dihedral : 5.961 58.827 603 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.07 % Allowed : 11.83 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.41 (0.36), residues: 547 helix: 1.79 (0.38), residues: 191 sheet: -0.68 (0.45), residues: 143 loop : -1.92 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 132 HIS 0.003 0.001 HIS B 55 PHE 0.019 0.001 PHE P 269 TYR 0.018 0.001 TYR P 173 ARG 0.004 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 215) hydrogen bonds : angle 4.94944 ( 603) SS BOND : bond 0.00448 ( 2) SS BOND : angle 0.53612 ( 4) covalent geometry : bond 0.00320 ( 4489) covalent geometry : angle 0.56068 ( 6122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.497 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8179 (tp) cc_final: 0.7739 (tp) REVERT: P 148 MET cc_start: 0.8486 (ttp) cc_final: 0.8187 (tmm) REVERT: B 4 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8259 (mmm) REVERT: B 81 GLU cc_start: 0.7971 (mp0) cc_final: 0.7693 (mp0) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.1363 time to fit residues: 11.9006 Evaluate side-chains 62 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain B residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.133274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.098180 restraints weight = 5351.298| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.25 r_work: 0.2866 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4491 Z= 0.128 Angle : 0.542 6.328 6126 Z= 0.283 Chirality : 0.043 0.166 693 Planarity : 0.004 0.059 765 Dihedral : 5.872 59.120 603 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.66 % Allowed : 14.73 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.29 (0.37), residues: 547 helix: 1.95 (0.38), residues: 191 sheet: -0.69 (0.45), residues: 143 loop : -1.85 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.002 0.000 HIS B 55 PHE 0.015 0.001 PHE P 269 TYR 0.014 0.001 TYR P 173 ARG 0.006 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 215) hydrogen bonds : angle 4.70641 ( 603) SS BOND : bond 0.00429 ( 2) SS BOND : angle 0.30620 ( 4) covalent geometry : bond 0.00295 ( 4489) covalent geometry : angle 0.54178 ( 6122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.467 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8089 (tp) cc_final: 0.7658 (tp) REVERT: P 148 MET cc_start: 0.8469 (ttp) cc_final: 0.8026 (tmm) REVERT: B 4 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8197 (mmm) REVERT: B 81 GLU cc_start: 0.7932 (mp0) cc_final: 0.7648 (mp0) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.1299 time to fit residues: 10.3896 Evaluate side-chains 57 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 4 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.133545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.098463 restraints weight = 5474.505| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.27 r_work: 0.2886 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4491 Z= 0.126 Angle : 0.539 6.126 6126 Z= 0.282 Chirality : 0.043 0.164 693 Planarity : 0.004 0.056 765 Dihedral : 5.257 53.238 600 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.45 % Allowed : 15.15 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.16 (0.37), residues: 547 helix: 2.06 (0.38), residues: 191 sheet: -0.61 (0.45), residues: 143 loop : -1.78 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.002 0.000 HIS B 55 PHE 0.012 0.001 PHE P 269 TYR 0.013 0.001 TYR P 173 ARG 0.003 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 215) hydrogen bonds : angle 4.58607 ( 603) SS BOND : bond 0.00446 ( 2) SS BOND : angle 0.24943 ( 4) covalent geometry : bond 0.00290 ( 4489) covalent geometry : angle 0.53871 ( 6122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.454 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8083 (tp) cc_final: 0.7674 (tp) REVERT: P 148 MET cc_start: 0.8438 (ttp) cc_final: 0.7926 (tmm) REVERT: B 81 GLU cc_start: 0.7917 (mp0) cc_final: 0.7635 (mp0) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.1094 time to fit residues: 8.9388 Evaluate side-chains 57 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 307 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0670 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.133556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.098680 restraints weight = 5309.456| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.24 r_work: 0.2887 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4491 Z= 0.127 Angle : 0.536 7.935 6126 Z= 0.279 Chirality : 0.043 0.164 693 Planarity : 0.004 0.055 765 Dihedral : 5.240 53.381 600 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.66 % Allowed : 16.18 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.01 (0.37), residues: 547 helix: 2.09 (0.37), residues: 195 sheet: -0.50 (0.46), residues: 143 loop : -1.70 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 132 HIS 0.002 0.000 HIS B 55 PHE 0.010 0.001 PHE P 269 TYR 0.012 0.001 TYR P 134 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 215) hydrogen bonds : angle 4.48673 ( 603) SS BOND : bond 0.00452 ( 2) SS BOND : angle 0.28244 ( 4) covalent geometry : bond 0.00293 ( 4489) covalent geometry : angle 0.53587 ( 6122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.484 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8082 (tp) cc_final: 0.7680 (tp) REVERT: P 148 MET cc_start: 0.8424 (ttp) cc_final: 0.7903 (tmm) REVERT: P 318 LEU cc_start: 0.7731 (pp) cc_final: 0.7432 (tp) REVERT: B 4 MET cc_start: 0.8629 (mmm) cc_final: 0.8163 (mmm) REVERT: B 81 GLU cc_start: 0.7986 (mp0) cc_final: 0.7629 (mp0) outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.1258 time to fit residues: 9.9511 Evaluate side-chains 58 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.095912 restraints weight = 5398.788| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.24 r_work: 0.2830 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4491 Z= 0.169 Angle : 0.573 7.817 6126 Z= 0.297 Chirality : 0.044 0.173 693 Planarity : 0.004 0.054 765 Dihedral : 5.396 53.362 600 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.28 % Allowed : 16.18 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.13 (0.37), residues: 547 helix: 2.02 (0.37), residues: 195 sheet: -0.58 (0.44), residues: 151 loop : -1.83 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 35 HIS 0.003 0.001 HIS B 55 PHE 0.012 0.001 PHE P 207 TYR 0.014 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 215) hydrogen bonds : angle 4.56392 ( 603) SS BOND : bond 0.00501 ( 2) SS BOND : angle 0.52917 ( 4) covalent geometry : bond 0.00408 ( 4489) covalent geometry : angle 0.57285 ( 6122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.482 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.5643 (t80) REVERT: P 140 ILE cc_start: 0.8100 (tp) cc_final: 0.7707 (tp) REVERT: P 148 MET cc_start: 0.8464 (ttp) cc_final: 0.7926 (tmm) REVERT: P 318 LEU cc_start: 0.7778 (pp) cc_final: 0.7388 (tp) REVERT: B 81 GLU cc_start: 0.8039 (mp0) cc_final: 0.7670 (mp0) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.1282 time to fit residues: 10.3058 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.134972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.099915 restraints weight = 5297.509| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.26 r_work: 0.2903 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4491 Z= 0.110 Angle : 0.520 7.256 6126 Z= 0.272 Chirality : 0.042 0.162 693 Planarity : 0.004 0.053 765 Dihedral : 5.223 54.154 600 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.28 % Allowed : 16.39 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.12 (0.37), residues: 547 helix: 2.21 (0.37), residues: 195 sheet: -0.46 (0.46), residues: 143 loop : -1.62 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 32 HIS 0.001 0.000 HIS B 55 PHE 0.010 0.001 PHE P 269 TYR 0.011 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 215) hydrogen bonds : angle 4.41729 ( 603) SS BOND : bond 0.00388 ( 2) SS BOND : angle 0.28677 ( 4) covalent geometry : bond 0.00245 ( 4489) covalent geometry : angle 0.51972 ( 6122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.425 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8046 (tp) cc_final: 0.7656 (tp) REVERT: P 148 MET cc_start: 0.8394 (ttp) cc_final: 0.7866 (tmm) REVERT: B 4 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8138 (mmm) REVERT: B 81 GLU cc_start: 0.7981 (mp0) cc_final: 0.7624 (mp0) outliers start: 11 outliers final: 9 residues processed: 57 average time/residue: 0.1275 time to fit residues: 10.0031 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.129579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.094451 restraints weight = 5415.277| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.22 r_work: 0.2824 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4491 Z= 0.208 Angle : 0.595 6.363 6126 Z= 0.312 Chirality : 0.045 0.179 693 Planarity : 0.004 0.053 765 Dihedral : 5.492 53.809 600 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.70 % Allowed : 16.18 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.08 (0.37), residues: 547 helix: 2.04 (0.36), residues: 196 sheet: -0.58 (0.44), residues: 151 loop : -1.78 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 35 HIS 0.004 0.001 HIS B 55 PHE 0.013 0.001 PHE P 207 TYR 0.015 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 215) hydrogen bonds : angle 4.57636 ( 603) SS BOND : bond 0.00578 ( 2) SS BOND : angle 0.62001 ( 4) covalent geometry : bond 0.00514 ( 4489) covalent geometry : angle 0.59484 ( 6122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.473 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.5906 (t80) REVERT: P 140 ILE cc_start: 0.8199 (tp) cc_final: 0.7813 (tp) REVERT: P 148 MET cc_start: 0.8389 (ttp) cc_final: 0.7929 (tmm) REVERT: B 81 GLU cc_start: 0.8039 (mp0) cc_final: 0.7674 (mp0) outliers start: 13 outliers final: 10 residues processed: 62 average time/residue: 0.1223 time to fit residues: 10.4547 Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.132273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.097050 restraints weight = 5257.227| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.22 r_work: 0.2845 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4491 Z= 0.140 Angle : 0.547 6.358 6126 Z= 0.289 Chirality : 0.043 0.172 693 Planarity : 0.004 0.054 765 Dihedral : 5.399 54.389 600 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.07 % Allowed : 16.80 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.04 (0.37), residues: 547 helix: 2.17 (0.36), residues: 195 sheet: -0.52 (0.46), residues: 143 loop : -1.68 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 245 HIS 0.002 0.000 HIS B 55 PHE 0.010 0.001 PHE P 87 TYR 0.013 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 215) hydrogen bonds : angle 4.49473 ( 603) SS BOND : bond 0.00557 ( 2) SS BOND : angle 0.19360 ( 4) covalent geometry : bond 0.00326 ( 4489) covalent geometry : angle 0.54728 ( 6122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.443 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.5574 (t80) REVERT: P 140 ILE cc_start: 0.8107 (tp) cc_final: 0.7723 (tp) REVERT: P 148 MET cc_start: 0.8309 (ttp) cc_final: 0.7847 (tmm) REVERT: B 81 GLU cc_start: 0.8005 (mp0) cc_final: 0.7642 (mp0) outliers start: 10 outliers final: 9 residues processed: 57 average time/residue: 0.2054 time to fit residues: 15.9003 Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.134712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.099752 restraints weight = 5382.050| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.23 r_work: 0.2882 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4491 Z= 0.118 Angle : 0.522 6.358 6126 Z= 0.276 Chirality : 0.042 0.163 693 Planarity : 0.004 0.053 765 Dihedral : 5.252 54.648 600 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.87 % Allowed : 17.43 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.15 (0.37), residues: 547 helix: 2.28 (0.36), residues: 195 sheet: -0.50 (0.46), residues: 143 loop : -1.60 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 32 HIS 0.001 0.000 HIS B 55 PHE 0.010 0.001 PHE P 269 TYR 0.012 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 215) hydrogen bonds : angle 4.33785 ( 603) SS BOND : bond 0.00446 ( 2) SS BOND : angle 0.17288 ( 4) covalent geometry : bond 0.00267 ( 4489) covalent geometry : angle 0.52239 ( 6122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2905.44 seconds wall clock time: 51 minutes 6.82 seconds (3066.82 seconds total)