Starting phenix.real_space_refine on Tue Mar 3 12:35:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dke_27488/03_2026/8dke_27488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dke_27488/03_2026/8dke_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_27488/03_2026/8dke_27488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dke_27488/03_2026/8dke_27488.map" model { file = "/net/cci-nas-00/data/ceres_data/8dke_27488/03_2026/8dke_27488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dke_27488/03_2026/8dke_27488.cif" } resolution = 3.18 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= 0.004 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.09, per 1000 atoms: 0.25 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: 0.29 Conformation dependent library (CDL) restraints added in 194.8 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: 0.11 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: 0.59 Time building geometry restraints manager: 0.43 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.000 ARG A 66 TYR 0.025 0.001 TYR P 173 PHE 0.035 0.001 PHE P 269 TRP 0.020 0.001 TRP P 132 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4489) covalent geometry : angle 0.74328 ( 6122) SS BOND : bond 0.00305 ( 2) SS BOND : angle 1.61714 ( 4) hydrogen bonds : bond 0.15974 ( 215) hydrogen bonds : angle 7.62770 ( 603) *********************** 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 : 0.161 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: 0.0618 time to fit residues: 4.6680 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 : 0.157 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.132825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.097942 restraints weight = 5391.842| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.20 r_work: 0.2884 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4491 Z= 0.156 Angle : 0.603 7.161 6126 Z= 0.315 Chirality : 0.044 0.197 693 Planarity : 0.005 0.073 765 Dihedral : 6.094 57.875 603 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.24 % Allowed : 10.37 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -0.67 (0.36), residues: 547 helix: 1.39 (0.38), residues: 194 sheet: -0.66 (0.46), residues: 137 loop : -2.01 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 73 TYR 0.022 0.001 TYR P 173 PHE 0.023 0.001 PHE P 269 TRP 0.011 0.001 TRP P 132 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4489) covalent geometry : angle 0.60190 ( 6122) SS BOND : bond 0.00388 ( 2) SS BOND : angle 1.34741 ( 4) hydrogen bonds : bond 0.04374 ( 215) hydrogen bonds : angle 5.38632 ( 603) *********************** 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 : 0.129 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.6052 (t80) REVERT: P 140 ILE cc_start: 0.8266 (tp) cc_final: 0.7872 (tt) REVERT: P 148 MET cc_start: 0.8476 (ttp) cc_final: 0.8021 (tmm) REVERT: B 81 GLU cc_start: 0.8067 (mp0) cc_final: 0.7814 (mp0) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.0595 time to fit residues: 5.2625 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 : 0.100 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.129768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.094522 restraints weight = 5404.615| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.21 r_work: 0.2806 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4491 Z= 0.195 Angle : 0.617 7.902 6126 Z= 0.320 Chirality : 0.045 0.183 693 Planarity : 0.004 0.065 765 Dihedral : 6.189 57.581 603 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.07 % Allowed : 12.86 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -0.63 (0.36), residues: 547 helix: 1.51 (0.37), residues: 197 sheet: -0.84 (0.43), residues: 151 loop : -2.05 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.021 0.001 TYR P 173 PHE 0.019 0.001 PHE P 269 TRP 0.010 0.001 TRP P 132 HIS 0.004 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 4489) covalent geometry : angle 0.61662 ( 6122) SS BOND : bond 0.00500 ( 2) SS BOND : angle 0.55611 ( 4) hydrogen bonds : bond 0.04584 ( 215) hydrogen bonds : angle 5.08764 ( 603) *********************** 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 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.147 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.5822 (t80) REVERT: P 140 ILE cc_start: 0.8159 (tp) cc_final: 0.7753 (tp) REVERT: P 148 MET cc_start: 0.8457 (ttp) cc_final: 0.8133 (tmm) REVERT: B 81 GLU cc_start: 0.8088 (mp0) cc_final: 0.7794 (mp0) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.0509 time to fit residues: 4.3843 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 : 0.097 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 42 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.129933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.094704 restraints weight = 5357.663| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.21 r_work: 0.2829 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4491 Z= 0.177 Angle : 0.592 7.741 6126 Z= 0.308 Chirality : 0.045 0.180 693 Planarity : 0.004 0.061 765 Dihedral : 6.102 54.746 603 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.49 % Allowed : 15.15 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -0.53 (0.36), residues: 547 helix: 1.63 (0.37), residues: 197 sheet: -0.83 (0.43), residues: 151 loop : -1.99 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.016 0.001 TYR P 173 PHE 0.015 0.001 PHE P 269 TRP 0.009 0.001 TRP P 132 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 4489) covalent geometry : angle 0.59257 ( 6122) SS BOND : bond 0.00470 ( 2) SS BOND : angle 0.31093 ( 4) hydrogen bonds : bond 0.04243 ( 215) hydrogen bonds : angle 4.86840 ( 603) *********************** 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 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.092 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.5798 (t80) REVERT: P 140 ILE cc_start: 0.8191 (tp) cc_final: 0.7772 (tp) REVERT: P 148 MET cc_start: 0.8488 (ttp) cc_final: 0.8170 (tmm) REVERT: B 81 GLU cc_start: 0.8085 (mp0) cc_final: 0.7802 (mp0) outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.0485 time to fit residues: 4.1127 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 A residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.0040 chunk 37 optimal weight: 0.7980 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.133846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.098820 restraints weight = 5347.078| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.24 r_work: 0.2872 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1414 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= 0.115 Angle : 0.536 6.468 6126 Z= 0.281 Chirality : 0.043 0.167 693 Planarity : 0.004 0.057 765 Dihedral : 5.353 54.182 600 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.83 % Allowed : 16.60 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -0.25 (0.37), residues: 547 helix: 1.85 (0.37), residues: 197 sheet: -0.68 (0.45), residues: 143 loop : -1.78 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.012 0.001 TYR P 134 PHE 0.012 0.001 PHE P 269 TRP 0.010 0.001 TRP B 32 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 4489) covalent geometry : angle 0.53591 ( 6122) SS BOND : bond 0.00569 ( 2) SS BOND : angle 0.32013 ( 4) hydrogen bonds : bond 0.03366 ( 215) hydrogen bonds : angle 4.62369 ( 603) *********************** 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: 4 poor density : 55 time to evaluate : 0.095 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8112 (tp) cc_final: 0.7711 (tp) REVERT: P 148 MET cc_start: 0.8494 (ttp) cc_final: 0.7973 (tmm) REVERT: B 81 GLU cc_start: 0.8088 (mp0) cc_final: 0.7735 (mp0) outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 0.0588 time to fit residues: 4.4383 Evaluate side-chains 56 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.130734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.095410 restraints weight = 5529.144| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.26 r_work: 0.2837 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4491 Z= 0.167 Angle : 0.577 7.265 6126 Z= 0.301 Chirality : 0.044 0.173 693 Planarity : 0.004 0.056 765 Dihedral : 5.462 53.881 600 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.37), residues: 547 helix: 1.84 (0.37), residues: 197 sheet: -0.72 (0.44), residues: 151 loop : -1.87 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.014 0.001 TYR P 134 PHE 0.011 0.001 PHE P 87 TRP 0.008 0.001 TRP P 132 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 4489) covalent geometry : angle 0.57723 ( 6122) SS BOND : bond 0.00575 ( 2) SS BOND : angle 0.27709 ( 4) hydrogen bonds : bond 0.03969 ( 215) hydrogen bonds : angle 4.62711 ( 603) *********************** 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 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.097 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.5720 (t80) REVERT: P 140 ILE cc_start: 0.8198 (tp) cc_final: 0.7796 (tp) REVERT: P 148 MET cc_start: 0.8498 (ttp) cc_final: 0.7965 (tmm) REVERT: B 81 GLU cc_start: 0.8010 (mp0) cc_final: 0.7656 (mp0) outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.0464 time to fit residues: 3.9351 Evaluate side-chains 57 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 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 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.132772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.097487 restraints weight = 5394.902| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.26 r_work: 0.2869 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1529 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= 0.132 Angle : 0.545 6.598 6126 Z= 0.285 Chirality : 0.043 0.168 693 Planarity : 0.004 0.055 765 Dihedral : 5.396 54.261 600 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.66 % Allowed : 17.84 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -0.11 (0.37), residues: 547 helix: 1.95 (0.37), residues: 197 sheet: -0.60 (0.46), residues: 143 loop : -1.69 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.012 0.001 TYR P 134 PHE 0.010 0.001 PHE P 269 TRP 0.008 0.001 TRP B 32 HIS 0.002 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4489) covalent geometry : angle 0.54533 ( 6122) SS BOND : bond 0.00526 ( 2) SS BOND : angle 0.13398 ( 4) hydrogen bonds : bond 0.03552 ( 215) hydrogen bonds : angle 4.53127 ( 603) *********************** 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 59 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.156 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8122 (tp) cc_final: 0.7729 (tp) REVERT: P 148 MET cc_start: 0.8465 (ttp) cc_final: 0.7927 (tmm) REVERT: B 81 GLU cc_start: 0.7972 (mp0) cc_final: 0.7606 (mp0) outliers start: 8 outliers final: 8 residues processed: 56 average time/residue: 0.0492 time to fit residues: 3.7731 Evaluate side-chains 57 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.132111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.096766 restraints weight = 5370.311| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.26 r_work: 0.2860 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1582 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= 0.144 Angle : 0.556 6.778 6126 Z= 0.290 Chirality : 0.044 0.169 693 Planarity : 0.004 0.054 765 Dihedral : 5.407 54.235 600 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.28 % Allowed : 17.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.37), residues: 547 helix: 1.98 (0.37), residues: 197 sheet: -0.52 (0.46), residues: 142 loop : -1.70 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.013 0.001 TYR P 134 PHE 0.010 0.001 PHE P 87 TRP 0.008 0.001 TRP P 132 HIS 0.002 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4489) covalent geometry : angle 0.55633 ( 6122) SS BOND : bond 0.00528 ( 2) SS BOND : angle 0.23325 ( 4) hydrogen bonds : bond 0.03683 ( 215) hydrogen bonds : angle 4.51122 ( 603) *********************** 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 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.143 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.5561 (t80) REVERT: P 140 ILE cc_start: 0.8096 (tp) cc_final: 0.7705 (tp) REVERT: P 148 MET cc_start: 0.8383 (ttp) cc_final: 0.7854 (tmm) REVERT: B 81 GLU cc_start: 0.7979 (mp0) cc_final: 0.7610 (mp0) outliers start: 11 outliers final: 9 residues processed: 56 average time/residue: 0.0571 time to fit residues: 4.2622 Evaluate side-chains 59 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 A residue 2 VAL Chi-restraints excluded: chain B residue 11 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 0.0020 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 overall best weight: 0.3446 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.136019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.100904 restraints weight = 5338.456| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.26 r_work: 0.2907 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4491 Z= 0.104 Angle : 0.512 6.050 6126 Z= 0.269 Chirality : 0.042 0.155 693 Planarity : 0.004 0.054 765 Dihedral : 5.219 54.677 600 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.49 % Allowed : 16.60 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: 0.16 (0.37), residues: 547 helix: 2.15 (0.37), residues: 197 sheet: -0.31 (0.47), residues: 138 loop : -1.62 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.011 0.001 TYR P 134 PHE 0.010 0.001 PHE P 269 TRP 0.010 0.001 TRP B 32 HIS 0.000 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 4489) covalent geometry : angle 0.51230 ( 6122) SS BOND : bond 0.00413 ( 2) SS BOND : angle 0.16543 ( 4) hydrogen bonds : bond 0.03015 ( 215) hydrogen bonds : angle 4.35056 ( 603) *********************** 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 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.138 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.7987 (tp) cc_final: 0.7575 (tp) REVERT: P 148 MET cc_start: 0.8361 (ttp) cc_final: 0.7877 (tmm) REVERT: P 318 LEU cc_start: 0.7613 (pp) cc_final: 0.7247 (tp) REVERT: B 81 GLU cc_start: 0.7931 (mp0) cc_final: 0.7574 (mp0) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.0474 time to fit residues: 3.9699 Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 269 PHE Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7818 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.132777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.097680 restraints weight = 5310.571| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.23 r_work: 0.2857 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1663 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= 0.146 Angle : 0.554 6.669 6126 Z= 0.288 Chirality : 0.044 0.167 693 Planarity : 0.004 0.054 765 Dihedral : 5.322 54.130 600 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.28 % Allowed : 17.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.37), residues: 547 helix: 2.08 (0.36), residues: 197 sheet: -0.47 (0.46), residues: 143 loop : -1.59 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.013 0.001 TYR P 134 PHE 0.010 0.001 PHE P 87 TRP 0.009 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4489) covalent geometry : angle 0.55445 ( 6122) SS BOND : bond 0.00557 ( 2) SS BOND : angle 0.57010 ( 4) hydrogen bonds : bond 0.03624 ( 215) hydrogen bonds : angle 4.42546 ( 603) ********************** 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 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.168 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.5528 (t80) REVERT: P 140 ILE cc_start: 0.8072 (tp) cc_final: 0.7686 (tp) REVERT: P 148 MET cc_start: 0.8386 (ttp) cc_final: 0.7888 (tmm) REVERT: B 81 GLU cc_start: 0.7968 (mp0) cc_final: 0.7609 (mp0) outliers start: 11 outliers final: 10 residues processed: 58 average time/residue: 0.0422 time to fit residues: 3.4827 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 : 0.142 ------------------------------------------------------------------------------- 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 269 PHE Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.134612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.099494 restraints weight = 5382.678| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.26 r_work: 0.2883 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1714 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= 0.114 Angle : 0.527 6.283 6126 Z= 0.276 Chirality : 0.042 0.161 693 Planarity : 0.004 0.054 765 Dihedral : 5.256 54.413 600 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.28 % Allowed : 17.22 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: 0.16 (0.37), residues: 547 helix: 2.16 (0.37), residues: 197 sheet: -0.45 (0.46), residues: 143 loop : -1.53 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.012 0.001 TYR P 134 PHE 0.009 0.001 PHE P 269 TRP 0.008 0.001 TRP B 32 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 4489) covalent geometry : angle 0.52747 ( 6122) SS BOND : bond 0.00446 ( 2) SS BOND : angle 0.15319 ( 4) hydrogen bonds : bond 0.03257 ( 215) hydrogen bonds : angle 4.38091 ( 603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1314.79 seconds wall clock time: 23 minutes 17.59 seconds (1397.59 seconds total)