Starting phenix.real_space_refine on Sun Mar 10 19:28:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/03_2024/8dke_27488.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/03_2024/8dke_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/03_2024/8dke_27488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/03_2024/8dke_27488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/03_2024/8dke_27488.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/03_2024/8dke_27488.pdb" } 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 Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.03, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 1.77 Conformation dependent library (CDL) restraints added in 787.1 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: 0.50 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: 1.21 Time building geometry restraints manager: 1.93 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: 88.78 - 97.83: 1 97.83 - 106.87: 126 106.87 - 115.92: 2755 115.92 - 124.96: 3151 124.96 - 134.01: 89 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 2.440 nonbonded pdb=" O SER A 52 " pdb=" NH1 ARG A 73 " model vdw 2.278 2.520 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 2.440 ... (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 ========== 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.760 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.010 Find NCS groups from input model: 0.130 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- 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 4489 Z= 0.206 Angle : 0.743 21.719 6122 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.468 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: 0.1550 time to fit residues: 11.8118 Evaluate side-chains 55 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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: 0.0870 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4489 Z= 0.273 Angle : 0.608 7.139 6122 Z= 0.317 Chirality : 0.045 0.215 693 Planarity : 0.005 0.074 765 Dihedral : 6.090 57.085 603 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.45 % Allowed : 10.37 % Favored : 88.17 % 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: -0.70 (0.36), residues: 547 helix: 1.32 (0.37), residues: 197 sheet: -0.75 (0.44), residues: 146 loop : -2.03 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 132 HIS 0.003 0.001 HIS B 55 PHE 0.024 0.001 PHE P 269 TYR 0.022 0.002 TYR P 173 ARG 0.002 0.000 ARG A 66 *********************** 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 67 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.524 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.5733 (t80) REVERT: P 140 ILE cc_start: 0.8188 (tp) cc_final: 0.7841 (tt) REVERT: P 148 MET cc_start: 0.8478 (ttp) cc_final: 0.8205 (tmm) REVERT: P 193 LYS cc_start: 0.8129 (tptp) cc_final: 0.7919 (tptm) REVERT: B 81 GLU cc_start: 0.7870 (mp0) cc_final: 0.7612 (mp0) outliers start: 7 outliers final: 5 residues processed: 65 average time/residue: 0.1571 time to fit residues: 13.3341 Evaluate side-chains 63 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 68 THR 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 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.0470 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4489 Z= 0.184 Angle : 0.540 6.396 6122 Z= 0.282 Chirality : 0.043 0.169 693 Planarity : 0.004 0.064 765 Dihedral : 5.864 55.502 603 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.87 % Allowed : 11.83 % Favored : 86.31 % 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: -0.44 (0.36), residues: 547 helix: 1.64 (0.37), residues: 197 sheet: -0.69 (0.45), residues: 143 loop : -1.91 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 PHE 0.018 0.001 PHE P 269 TYR 0.014 0.001 TYR P 173 ARG 0.004 0.000 ARG A 66 *********************** 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 69 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.468 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8095 (tp) cc_final: 0.7694 (tp) REVERT: P 148 MET cc_start: 0.8455 (ttp) cc_final: 0.8049 (tmm) REVERT: B 4 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8210 (mmm) REVERT: B 81 GLU cc_start: 0.7938 (mp0) cc_final: 0.7669 (mp0) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 0.1378 time to fit residues: 12.1334 Evaluate side-chains 61 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 B residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4489 Z= 0.227 Angle : 0.556 6.930 6122 Z= 0.289 Chirality : 0.043 0.172 693 Planarity : 0.004 0.060 765 Dihedral : 5.334 52.745 600 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.70 % Allowed : 13.28 % Favored : 84.02 % 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: -0.34 (0.37), residues: 547 helix: 1.75 (0.37), residues: 197 sheet: -0.62 (0.45), residues: 142 loop : -1.90 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 PHE 0.014 0.001 PHE P 269 TYR 0.016 0.001 TYR P 173 ARG 0.002 0.000 ARG A 66 *********************** 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 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.543 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8124 (tp) cc_final: 0.7747 (tp) REVERT: P 148 MET cc_start: 0.8385 (ttp) cc_final: 0.7978 (tmm) REVERT: B 4 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8209 (mmm) REVERT: B 81 GLU cc_start: 0.7961 (mp0) cc_final: 0.7672 (mp0) outliers start: 13 outliers final: 8 residues processed: 63 average time/residue: 0.1394 time to fit residues: 11.8540 Evaluate side-chains 63 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 68 THR 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 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 34 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4489 Z= 0.249 Angle : 0.566 6.992 6122 Z= 0.295 Chirality : 0.044 0.174 693 Planarity : 0.004 0.057 765 Dihedral : 5.417 53.044 600 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.49 % Allowed : 15.35 % 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: -0.29 (0.37), residues: 547 helix: 1.88 (0.37), residues: 197 sheet: -0.67 (0.44), residues: 151 loop : -1.94 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 PHE 0.011 0.001 PHE P 269 TYR 0.014 0.001 TYR P 173 ARG 0.005 0.000 ARG A 66 *********************** 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 67 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 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: 0.8127 (tp) cc_final: 0.7783 (tp) REVERT: P 148 MET cc_start: 0.8361 (ttp) cc_final: 0.7953 (tmm) REVERT: B 4 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8184 (mmm) REVERT: B 81 GLU cc_start: 0.7974 (mp0) cc_final: 0.7665 (mp0) outliers start: 12 outliers final: 10 residues processed: 63 average time/residue: 0.1390 time to fit residues: 11.8402 Evaluate side-chains 65 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 68 THR 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 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 34 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 0.0770 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4489 Z= 0.191 Angle : 0.534 6.363 6122 Z= 0.279 Chirality : 0.043 0.167 693 Planarity : 0.004 0.055 765 Dihedral : 5.306 53.462 600 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.07 % Allowed : 17.43 % 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 (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: -0.11 (0.37), residues: 547 helix: 2.03 (0.37), residues: 197 sheet: -0.60 (0.46), residues: 143 loop : -1.79 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.003 0.000 ARG A 66 *********************** 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 fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.505 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8020 (tp) cc_final: 0.7651 (tp) REVERT: P 148 MET cc_start: 0.8313 (ttp) cc_final: 0.7911 (tmm) REVERT: B 81 GLU cc_start: 0.7975 (mp0) cc_final: 0.7680 (mp0) outliers start: 10 outliers final: 8 residues processed: 61 average time/residue: 0.1404 time to fit residues: 11.5181 Evaluate side-chains 62 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 68 THR 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 34 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4489 Z= 0.202 Angle : 0.537 8.091 6122 Z= 0.279 Chirality : 0.043 0.167 693 Planarity : 0.004 0.055 765 Dihedral : 5.313 53.534 600 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.90 % Allowed : 18.05 % Favored : 79.05 % 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 (0.37), residues: 195 sheet: -0.55 (0.46), residues: 143 loop : -1.81 (0.41), residues: 209 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 0.010 0.001 PHE P 87 TYR 0.012 0.001 TYR P 134 ARG 0.003 0.000 ARG A 66 *********************** 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 70 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.533 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8006 (tp) cc_final: 0.7647 (tp) REVERT: P 148 MET cc_start: 0.8318 (ttp) cc_final: 0.7912 (tmm) REVERT: P 318 LEU cc_start: 0.7806 (pp) cc_final: 0.7477 (tp) REVERT: B 4 MET cc_start: 0.8657 (mmm) cc_final: 0.8252 (mmm) REVERT: B 81 GLU cc_start: 0.7984 (mp0) cc_final: 0.7680 (mp0) outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 0.1368 time to fit residues: 12.3332 Evaluate side-chains 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 68 THR 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 303 LEU Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 34 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.0470 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4489 Z= 0.201 Angle : 0.536 7.971 6122 Z= 0.278 Chirality : 0.043 0.166 693 Planarity : 0.004 0.054 765 Dihedral : 5.298 53.666 600 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.28 % Allowed : 18.46 % Favored : 79.25 % 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: 0.02 (0.37), residues: 547 helix: 2.22 (0.37), residues: 195 sheet: -0.53 (0.46), residues: 143 loop : -1.79 (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 87 TYR 0.012 0.001 TYR P 134 ARG 0.003 0.000 ARG A 66 *********************** 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 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.489 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.7997 (tp) cc_final: 0.7641 (tp) REVERT: P 148 MET cc_start: 0.8336 (ttp) cc_final: 0.7929 (tmm) REVERT: P 318 LEU cc_start: 0.7772 (pp) cc_final: 0.7475 (tp) REVERT: B 4 MET cc_start: 0.8650 (mmm) cc_final: 0.8239 (mmm) REVERT: B 81 GLU cc_start: 0.7988 (mp0) cc_final: 0.7683 (mp0) outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.1385 time to fit residues: 12.1105 Evaluate side-chains 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 68 THR 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 34 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4489 Z= 0.255 Angle : 0.563 8.226 6122 Z= 0.292 Chirality : 0.044 0.173 693 Planarity : 0.004 0.054 765 Dihedral : 5.408 53.655 600 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.70 % Allowed : 19.09 % Favored : 78.22 % 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: -0.07 (0.37), residues: 547 helix: 2.14 (0.37), residues: 196 sheet: -0.54 (0.44), residues: 151 loop : -1.90 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 35 HIS 0.002 0.001 HIS B 55 PHE 0.011 0.001 PHE P 87 TYR 0.013 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 *********************** 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 72 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.448 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.5427 (t80) REVERT: P 140 ILE cc_start: 0.8017 (tp) cc_final: 0.7666 (tp) REVERT: P 148 MET cc_start: 0.8346 (ttp) cc_final: 0.7920 (tmm) REVERT: P 318 LEU cc_start: 0.7832 (pp) cc_final: 0.7453 (tp) REVERT: B 81 GLU cc_start: 0.7993 (mp0) cc_final: 0.7658 (mp0) outliers start: 13 outliers final: 12 residues processed: 66 average time/residue: 0.1350 time to fit residues: 11.9653 Evaluate side-chains 71 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 68 THR 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 34 ASN 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 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.0770 chunk 45 optimal weight: 0.0030 chunk 13 optimal weight: 0.0270 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4489 Z= 0.139 Angle : 0.506 7.369 6122 Z= 0.264 Chirality : 0.041 0.156 693 Planarity : 0.004 0.053 765 Dihedral : 5.192 54.623 600 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.07 % Allowed : 19.50 % Favored : 78.42 % 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: 0.17 (0.37), residues: 547 helix: 2.31 (0.37), residues: 197 sheet: -0.43 (0.46), residues: 143 loop : -1.69 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 32 HIS 0.001 0.000 HIS P 211 PHE 0.009 0.001 PHE P 269 TYR 0.011 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 ********************** 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 65 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.491 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.7856 (tp) cc_final: 0.7470 (tp) REVERT: P 148 MET cc_start: 0.8331 (ttp) cc_final: 0.7943 (ppp) REVERT: B 4 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8195 (mmm) REVERT: B 81 GLU cc_start: 0.7927 (mp0) cc_final: 0.7616 (mp0) outliers start: 10 outliers final: 9 residues processed: 61 average time/residue: 0.1450 time to fit residues: 11.8678 Evaluate side-chains 63 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.0170 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.0570 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 = 0.135043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.100458 restraints weight = 5323.684| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.20 r_work: 0.2893 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 0.030 4489 Z= 0.178 Angle : 0.509 5.933 6122 Z= 0.267 Chirality : 0.042 0.158 693 Planarity : 0.004 0.054 765 Dihedral : 5.184 54.342 600 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.28 % Allowed : 19.50 % Favored : 78.22 % 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: 0.20 (0.37), residues: 547 helix: 2.40 (0.37), residues: 195 sheet: -0.41 (0.46), residues: 143 loop : -1.72 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 32 HIS 0.002 0.000 HIS B 55 PHE 0.009 0.001 PHE P 269 TYR 0.012 0.001 TYR P 134 ARG 0.003 0.000 ARG A 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1313.40 seconds wall clock time: 24 minutes 20.85 seconds (1460.85 seconds total)