Starting phenix.real_space_refine on Mon Sep 23 18:07:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/09_2024/8dke_27488.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/09_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_27488/09_2024/8dke_27488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/09_2024/8dke_27488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/09_2024/8dke_27488.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dke_27488/09_2024/8dke_27488.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2861 2.51 5 N 704 2.21 5 O 789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.43, per 1000 atoms: 0.79 Number of scatterers: 4369 At special positions: 0 Unit cell: (83.358, 63.992, 120.406, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 789 8.00 N 704 7.00 C 2861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 558.6 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: 0.49 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: 1.17 Time building geometry restraints manager: 1.55 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: 0.010 Normalize map: mean=0, sd=1: 2.690 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.170 Find NCS groups from input model: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.040 ------------------------------------------------------------------------------- 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 : 0.519 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: 0.1567 time to fit residues: 11.8903 Evaluate side-chains 55 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain A residue 42 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4489 Z= 0.189 Angle : 0.577 7.063 6122 Z= 0.303 Chirality : 0.043 0.176 693 Planarity : 0.004 0.074 765 Dihedral : 5.995 58.601 603 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.24 % Allowed : 9.75 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.36), residues: 547 helix: 1.44 (0.38), residues: 194 sheet: -0.70 (0.46), residues: 138 loop : -1.98 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 PHE 0.024 0.001 PHE P 269 TYR 0.019 0.001 TYR P 173 ARG 0.006 0.000 ARG A 73 *********************** 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 fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.453 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.5573 (t80) REVERT: P 140 ILE cc_start: 0.8136 (tp) cc_final: 0.7809 (tt) REVERT: P 148 MET cc_start: 0.8474 (ttp) cc_final: 0.7998 (tmm) REVERT: P 193 LYS cc_start: 0.8106 (tptp) cc_final: 0.7895 (tptm) REVERT: B 81 GLU cc_start: 0.7870 (mp0) cc_final: 0.7627 (mp0) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1492 time to fit residues: 13.2770 Evaluate side-chains 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.0020 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.3906 ------------------------------------------------------------------------------- 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: 0.8181 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4489 Z= 0.156 Angle : 0.528 6.082 6122 Z= 0.277 Chirality : 0.042 0.162 693 Planarity : 0.004 0.062 765 Dihedral : 5.784 56.784 603 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.87 % Allowed : 11.41 % Favored : 86.72 % 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: 1.87 (0.38), residues: 191 sheet: -0.66 (0.45), residues: 143 loop : -1.89 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 132 HIS 0.002 0.000 HIS B 55 PHE 0.020 0.001 PHE P 269 TYR 0.014 0.001 TYR P 173 ARG 0.004 0.000 ARG A 73 *********************** 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 71 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.488 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8052 (tp) cc_final: 0.7637 (tp) REVERT: P 148 MET cc_start: 0.8512 (ttp) cc_final: 0.8074 (tmm) REVERT: B 4 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8301 (mmm) REVERT: B 81 GLU cc_start: 0.7719 (mp0) cc_final: 0.7473 (mp0) outliers start: 9 outliers final: 5 residues processed: 67 average time/residue: 0.1567 time to fit residues: 13.6453 Evaluate side-chains 64 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 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: 0.8231 moved from start: 0.1339 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= 0.224 Angle : 0.559 7.858 6122 Z= 0.289 Chirality : 0.043 0.167 693 Planarity : 0.004 0.059 765 Dihedral : 5.819 57.704 603 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.87 % Allowed : 14.11 % 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: -0.24 (0.37), residues: 547 helix: 1.86 (0.37), residues: 195 sheet: -0.60 (0.45), residues: 143 loop : -1.82 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.003 0.001 HIS B 55 PHE 0.014 0.001 PHE P 269 TYR 0.016 0.001 TYR P 173 ARG 0.005 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 62 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.500 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8052 (tp) cc_final: 0.7679 (tp) REVERT: P 148 MET cc_start: 0.8440 (ttp) cc_final: 0.7988 (tmm) REVERT: P 318 LEU cc_start: 0.7816 (pp) cc_final: 0.7451 (tp) REVERT: B 4 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8264 (mmm) REVERT: B 81 GLU cc_start: 0.7721 (mp0) cc_final: 0.7449 (mp0) outliers start: 9 outliers final: 5 residues processed: 59 average time/residue: 0.1289 time to fit residues: 10.5452 Evaluate side-chains 57 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8273 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4489 Z= 0.310 Angle : 0.601 8.124 6122 Z= 0.312 Chirality : 0.045 0.179 693 Planarity : 0.004 0.057 765 Dihedral : 5.473 53.209 600 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.28 % Allowed : 14.73 % Favored : 82.99 % 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: -0.31 (0.37), residues: 547 helix: 1.82 (0.37), residues: 196 sheet: -0.68 (0.43), residues: 151 loop : -1.88 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 35 HIS 0.003 0.001 HIS B 55 PHE 0.013 0.001 PHE P 207 TYR 0.016 0.001 TYR P 173 ARG 0.006 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 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 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 134 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.5484 (t80) REVERT: P 140 ILE cc_start: 0.8126 (tp) cc_final: 0.7770 (tp) REVERT: P 148 MET cc_start: 0.8485 (ttp) cc_final: 0.7985 (tmm) REVERT: A 66 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8090 (ttm170) REVERT: B 81 GLU cc_start: 0.7783 (mp0) cc_final: 0.7515 (mp0) outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.1284 time to fit residues: 10.9616 Evaluate side-chains 61 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 238 ILE 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 10 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4489 Z= 0.186 Angle : 0.539 7.945 6122 Z= 0.282 Chirality : 0.043 0.168 693 Planarity : 0.004 0.055 765 Dihedral : 5.285 53.901 600 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.87 % Allowed : 15.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.37), residues: 547 helix: 2.06 (0.37), residues: 195 sheet: -0.59 (0.45), 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 0.011 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 60 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.500 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8094 (tp) cc_final: 0.7738 (tp) REVERT: P 148 MET cc_start: 0.8395 (ttp) cc_final: 0.7932 (tmm) REVERT: P 318 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7505 (tp) REVERT: B 81 GLU cc_start: 0.7808 (mp0) cc_final: 0.7476 (mp0) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.1382 time to fit residues: 10.3316 Evaluate side-chains 57 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain P residue 318 LEU 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 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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: 0.8228 moved from start: 0.1599 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= 0.195 Angle : 0.540 8.048 6122 Z= 0.281 Chirality : 0.043 0.166 693 Planarity : 0.004 0.054 765 Dihedral : 5.251 53.996 600 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.70 % Allowed : 15.56 % Favored : 81.74 % 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: -0.06 (0.37), residues: 547 helix: 2.11 (0.37), residues: 195 sheet: -0.78 (0.45), residues: 153 loop : -1.62 (0.42), residues: 199 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 269 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 62 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.453 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.8059 (tp) cc_final: 0.7704 (tp) REVERT: P 148 MET cc_start: 0.8395 (ttp) cc_final: 0.7936 (tmm) REVERT: P 318 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7480 (tp) REVERT: B 4 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8164 (mmm) REVERT: B 81 GLU cc_start: 0.7773 (mp0) cc_final: 0.7442 (mp0) outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 0.1311 time to fit residues: 10.0426 Evaluate side-chains 60 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 P residue 318 LEU Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.8286 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4489 Z= 0.340 Angle : 0.611 9.016 6122 Z= 0.317 Chirality : 0.046 0.183 693 Planarity : 0.004 0.054 765 Dihedral : 5.535 53.861 600 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.70 % Allowed : 16.39 % 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 (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: -0.26 (0.37), residues: 547 helix: 1.95 (0.36), residues: 196 sheet: -0.90 (0.42), residues: 162 loop : -1.75 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 35 HIS 0.004 0.001 HIS B 55 PHE 0.013 0.001 PHE P 207 TYR 0.015 0.001 TYR P 134 ARG 0.004 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 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.503 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.5634 (t80) REVERT: P 140 ILE cc_start: 0.8149 (tp) cc_final: 0.7812 (tp) REVERT: P 148 MET cc_start: 0.8432 (ttp) cc_final: 0.7933 (tmm) REVERT: B 81 GLU cc_start: 0.7817 (mp0) cc_final: 0.7480 (mp0) outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.1230 time to fit residues: 10.4743 Evaluate side-chains 63 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8234 moved from start: 0.1675 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= 0.194 Angle : 0.550 8.545 6122 Z= 0.286 Chirality : 0.043 0.171 693 Planarity : 0.004 0.054 765 Dihedral : 5.368 54.556 600 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.07 % Allowed : 17.01 % 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 (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: -0.06 (0.37), residues: 547 helix: 2.13 (0.37), residues: 195 sheet: -0.79 (0.45), residues: 153 loop : -1.62 (0.42), residues: 199 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 0.007 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 59 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.522 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 134 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.5326 (t80) REVERT: P 140 ILE cc_start: 0.8083 (tp) cc_final: 0.7741 (tp) REVERT: P 148 MET cc_start: 0.8389 (ttp) cc_final: 0.7928 (tmm) REVERT: B 81 GLU cc_start: 0.7815 (mp0) cc_final: 0.7467 (mp0) outliers start: 10 outliers final: 9 residues processed: 55 average time/residue: 0.1363 time to fit residues: 10.4054 Evaluate side-chains 58 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 0.0570 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.0370 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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: 0.8187 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4489 Z= 0.151 Angle : 0.519 8.128 6122 Z= 0.271 Chirality : 0.042 0.157 693 Planarity : 0.004 0.053 765 Dihedral : 5.164 54.811 600 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 : 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 (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: 0.18 (0.38), residues: 547 helix: 2.28 (0.37), residues: 195 sheet: -0.54 (0.46), residues: 148 loop : -1.54 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 32 HIS 0.001 0.000 HIS B 55 PHE 0.010 0.001 PHE P 269 TYR 0.011 0.001 TYR P 134 ARG 0.003 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 61 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.545 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.7988 (tp) cc_final: 0.7650 (tp) REVERT: P 148 MET cc_start: 0.8337 (ttp) cc_final: 0.7908 (tmm) REVERT: B 4 MET cc_start: 0.8575 (mmm) cc_final: 0.7955 (mmm) REVERT: B 81 GLU cc_start: 0.7765 (mp0) cc_final: 0.7425 (mp0) outliers start: 8 outliers final: 8 residues processed: 58 average time/residue: 0.1160 time to fit residues: 9.3743 Evaluate side-chains 60 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.0170 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.0470 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.136286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.101048 restraints weight = 5309.916| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.27 r_work: 0.2932 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1841 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= 0.160 Angle : 0.519 8.124 6122 Z= 0.270 Chirality : 0.042 0.155 693 Planarity : 0.004 0.053 765 Dihedral : 5.132 54.498 600 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.07 % Allowed : 17.63 % Favored : 80.29 % 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: 0.27 (0.38), residues: 547 helix: 2.32 (0.37), residues: 195 sheet: -0.47 (0.46), residues: 148 loop : -1.45 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1336.76 seconds wall clock time: 24 minutes 22.02 seconds (1462.02 seconds total)