Starting phenix.real_space_refine on Thu Jul 18 22:51:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkx_27493/07_2024/8dkx_27493.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkx_27493/07_2024/8dkx_27493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkx_27493/07_2024/8dkx_27493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkx_27493/07_2024/8dkx_27493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkx_27493/07_2024/8dkx_27493.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkx_27493/07_2024/8dkx_27493.cif" } resolution = 3.0 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= 0.084 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 2863 2.51 5 N 704 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "P ASP 74": "OD1" <-> "OD2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 151": "NH1" <-> "NH2" Residue "P GLU 188": "OE1" <-> "OE2" Residue "P TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 295": "OE1" <-> "OE2" Residue "P PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4370 Number of models: 1 Model: "" Number of chains: 3 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 Chain: "P" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 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 Time building chain proxies: 3.24, per 1000 atoms: 0.74 Number of scatterers: 4370 At special positions: 0 Unit cell: (76.36, 63.91, 122.01, 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 788 8.00 N 704 7.00 C 2863 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=2.03 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: 1.55 Conformation dependent library (CDL) restraints added in 800.0 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: 10 helices and 9 sheets defined 35.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.794A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 139 removed outlier: 3.914A pdb=" N SER P 124 " --> pdb=" O SER P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 153 removed outlier: 4.187A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 182 Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 removed outlier: 3.591A pdb=" N VAL P 206 " --> pdb=" O ASN P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 258 Processing helix chain 'P' and resid 263 through 291 Proline residue: P 283 - end of helix removed outlier: 3.751A pdb=" N PHE P 289 " --> pdb=" O ALA P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 323 removed outlier: 3.554A pdb=" N PHE P 311 " --> pdb=" O THR P 307 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET P 316 " --> pdb=" O SER P 312 " (cutoff:3.500A) Processing helix chain 'P' and resid 338 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.423A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA A 33 " --> pdb=" O TYR A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.928A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.696A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.418A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'P' and resid 31 through 35 removed outlier: 6.805A pdb=" N VAL P 32 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE P 118 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU P 34 " --> pdb=" O ILE P 118 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 39 through 43 removed outlier: 3.513A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 54 through 56 218 hydrogen bonds defined for protein. 621 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: 1.05 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1343 1.34 - 1.46: 1039 1.46 - 1.58: 2086 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4490 Sorted by residual: bond pdb=" N GLY P 258 " pdb=" CA GLY P 258 " ideal model delta sigma weight residual 1.445 1.478 -0.033 8.30e-03 1.45e+04 1.60e+01 bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.17e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.32e-02 5.74e+03 4.56e+00 bond pdb=" N TRP P 262 " pdb=" CA TRP P 262 " ideal model delta sigma weight residual 1.460 1.485 -0.025 1.83e-02 2.99e+03 1.87e+00 ... (remaining 4485 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.52: 121 106.52 - 113.49: 2423 113.49 - 120.45: 1757 120.45 - 127.42: 1765 127.42 - 134.39: 56 Bond angle restraints: 6122 Sorted by residual: angle pdb=" N THR P 261 " pdb=" CA THR P 261 " pdb=" C THR P 261 " ideal model delta sigma weight residual 113.02 121.82 -8.80 1.20e+00 6.94e-01 5.38e+01 angle pdb=" N TRP P 262 " pdb=" CA TRP P 262 " pdb=" C TRP P 262 " ideal model delta sigma weight residual 113.20 99.56 13.64 2.08e+00 2.31e-01 4.30e+01 angle pdb=" N GLY P 258 " pdb=" CA GLY P 258 " pdb=" C GLY P 258 " ideal model delta sigma weight residual 111.20 119.74 -8.54 1.39e+00 5.18e-01 3.77e+01 angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 113.20 109.16 4.04 9.60e-01 1.09e+00 1.77e+01 angle pdb=" CA VAL P 259 " pdb=" C VAL P 259 " pdb=" O VAL P 259 " ideal model delta sigma weight residual 121.17 117.07 4.10 1.06e+00 8.90e-01 1.50e+01 ... (remaining 6117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 2312 17.22 - 34.44: 228 34.44 - 51.66: 37 51.66 - 68.88: 4 68.88 - 86.10: 2 Dihedral angle restraints: 2583 sinusoidal: 986 harmonic: 1597 Sorted by residual: dihedral pdb=" C ILE P 260 " pdb=" N ILE P 260 " pdb=" CA ILE P 260 " pdb=" CB ILE P 260 " ideal model delta harmonic sigma weight residual -122.00 -135.90 13.90 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" N ILE P 260 " pdb=" C ILE P 260 " pdb=" CA ILE P 260 " pdb=" CB ILE P 260 " ideal model delta harmonic sigma weight residual 123.40 135.21 -11.81 0 2.50e+00 1.60e-01 2.23e+01 dihedral pdb=" CA LYS P 335 " pdb=" C LYS P 335 " pdb=" N PHE P 336 " pdb=" CA PHE P 336 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 609 0.073 - 0.145: 80 0.145 - 0.218: 2 0.218 - 0.291: 0 0.291 - 0.363: 2 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA THR P 261 " pdb=" N THR P 261 " pdb=" C THR P 261 " pdb=" CB THR P 261 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA ILE P 260 " pdb=" N ILE P 260 " pdb=" C ILE P 260 " pdb=" CB ILE P 260 " both_signs ideal model delta sigma weight residual False 2.43 2.08 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB VAL P 259 " pdb=" CA VAL P 259 " pdb=" CG1 VAL P 259 " pdb=" CG2 VAL P 259 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 690 not shown) Planarity restraints: 764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 297 " 0.012 2.00e-02 2.50e+03 1.05e-02 2.75e+00 pdb=" CG TRP P 297 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP P 297 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP P 297 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 297 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 297 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 297 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 297 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 297 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 259 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C VAL P 259 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL P 259 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE P 260 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 43 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO B 44 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " -0.019 5.00e-02 4.00e+02 ... (remaining 761 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 70 2.66 - 3.22: 4081 3.22 - 3.78: 6520 3.78 - 4.34: 9227 4.34 - 4.90: 15449 Nonbonded interactions: 35347 Sorted by model distance: nonbonded pdb=" OH TYR P 134 " pdb=" OD1 ASP P 205 " model vdw 2.099 2.440 nonbonded pdb=" O SER A 52 " pdb=" NH1 ARG A 73 " model vdw 2.187 2.520 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR P 281 " pdb=" OD2 ASP P 305 " model vdw 2.245 2.440 ... (remaining 35342 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: 1.110 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.005 0.043 4490 Z= 0.290 Angle : 0.748 13.644 6122 Z= 0.436 Chirality : 0.049 0.363 693 Planarity : 0.004 0.033 764 Dihedral : 13.282 86.102 1557 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.62 % Allowed : 6.43 % Favored : 92.95 % Cbeta Deviations : 0.20 % 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: -3.42 (0.31), residues: 547 helix: -1.19 (0.31), residues: 204 sheet: -2.45 (0.37), residues: 161 loop : -3.10 (0.36), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP P 297 HIS 0.002 0.001 HIS B 55 PHE 0.020 0.001 PHE P 269 TYR 0.011 0.001 TYR B 49 ARG 0.004 0.000 ARG B 61 *********************** 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: 3 poor density : 57 time to evaluate : 0.495 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: B 82 ASP cc_start: 0.7840 (m-30) cc_final: 0.7598 (m-30) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.8397 time to fit residues: 52.3745 Evaluate side-chains 51 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain P residue 259 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 13 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN P 96 GLN P 149 ASN P 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4490 Z= 0.184 Angle : 0.586 9.950 6122 Z= 0.297 Chirality : 0.043 0.139 693 Planarity : 0.004 0.029 764 Dihedral : 5.688 57.931 599 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.28 % Allowed : 13.07 % Favored : 84.65 % 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: -1.92 (0.33), residues: 547 helix: 0.27 (0.35), residues: 206 sheet: -1.72 (0.40), residues: 147 loop : -2.51 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 297 HIS 0.002 0.000 HIS B 55 PHE 0.020 0.001 PHE A 69 TYR 0.017 0.001 TYR P 134 ARG 0.002 0.000 ARG P 112 *********************** 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 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.470 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 71 GLU cc_start: 0.7434 (tt0) cc_final: 0.7154 (tm-30) REVERT: P 269 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.5771 (m-10) outliers start: 11 outliers final: 5 residues processed: 62 average time/residue: 0.9263 time to fit residues: 60.4864 Evaluate side-chains 54 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.0000 chunk 39 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4490 Z= 0.190 Angle : 0.575 10.008 6122 Z= 0.289 Chirality : 0.043 0.138 693 Planarity : 0.003 0.027 764 Dihedral : 5.498 53.612 599 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.11 % Allowed : 14.32 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.35), residues: 547 helix: 0.86 (0.36), residues: 206 sheet: -1.26 (0.42), residues: 146 loop : -2.21 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 297 HIS 0.001 0.000 HIS P 211 PHE 0.026 0.001 PHE A 69 TYR 0.017 0.001 TYR P 134 ARG 0.005 0.000 ARG B 24 *********************** 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 63 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.429 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 13 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7867 (mmmt) REVERT: A 106 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7753 (mt) REVERT: B 79 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.8015 (mm-40) REVERT: P 71 GLU cc_start: 0.7392 (tt0) cc_final: 0.7139 (tm-30) REVERT: P 269 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.5857 (m-10) REVERT: P 282 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7338 (m-10) REVERT: P 318 LEU cc_start: 0.7457 (pp) cc_final: 0.7115 (tp) outliers start: 15 outliers final: 6 residues processed: 58 average time/residue: 0.9512 time to fit residues: 58.0125 Evaluate side-chains 58 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4490 Z= 0.219 Angle : 0.578 9.856 6122 Z= 0.290 Chirality : 0.043 0.142 693 Planarity : 0.003 0.029 764 Dihedral : 5.413 47.972 599 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.32 % Allowed : 16.80 % Favored : 79.88 % 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: -0.94 (0.35), residues: 547 helix: 1.07 (0.36), residues: 206 sheet: -1.06 (0.42), residues: 146 loop : -2.07 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 297 HIS 0.001 0.001 HIS B 55 PHE 0.017 0.001 PHE A 69 TYR 0.018 0.001 TYR P 134 ARG 0.004 0.000 ARG B 24 *********************** 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: 16 poor density : 52 time to evaluate : 0.493 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 106 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7754 (mt) REVERT: B 79 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8024 (mm-40) REVERT: P 71 GLU cc_start: 0.7403 (tt0) cc_final: 0.7150 (tm-30) REVERT: P 134 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7963 (p90) REVERT: P 269 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.5921 (m-10) REVERT: P 282 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7360 (m-10) outliers start: 16 outliers final: 7 residues processed: 64 average time/residue: 0.8413 time to fit residues: 56.9160 Evaluate side-chains 59 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 21 optimal weight: 0.0040 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4490 Z= 0.190 Angle : 0.567 10.553 6122 Z= 0.282 Chirality : 0.043 0.139 693 Planarity : 0.003 0.030 764 Dihedral : 5.207 41.117 599 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.15 % Allowed : 17.84 % Favored : 78.01 % 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: -0.71 (0.35), residues: 547 helix: 1.26 (0.36), residues: 206 sheet: -0.91 (0.42), residues: 146 loop : -1.99 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 297 HIS 0.001 0.000 HIS B 55 PHE 0.014 0.001 PHE A 69 TYR 0.017 0.001 TYR P 134 ARG 0.005 0.000 ARG B 24 *********************** 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 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 0.469 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 106 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7789 (mt) REVERT: P 71 GLU cc_start: 0.7317 (tt0) cc_final: 0.7078 (tm-30) REVERT: P 147 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7750 (mp) REVERT: P 269 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.5861 (m-10) REVERT: P 282 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7325 (m-10) REVERT: P 318 LEU cc_start: 0.7479 (pp) cc_final: 0.7178 (tp) outliers start: 20 outliers final: 8 residues processed: 64 average time/residue: 0.8665 time to fit residues: 58.5244 Evaluate side-chains 58 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4490 Z= 0.173 Angle : 0.552 9.993 6122 Z= 0.274 Chirality : 0.043 0.138 693 Planarity : 0.003 0.048 764 Dihedral : 5.010 33.453 599 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.94 % Allowed : 18.46 % Favored : 77.59 % 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: -0.53 (0.35), residues: 547 helix: 1.37 (0.36), residues: 207 sheet: -0.78 (0.42), residues: 146 loop : -1.87 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 297 HIS 0.001 0.000 HIS P 211 PHE 0.011 0.001 PHE A 69 TYR 0.016 0.001 TYR P 134 ARG 0.012 0.001 ARG B 24 *********************** 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 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 0.421 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: B 11 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7526 (pp) REVERT: P 134 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7881 (p90) REVERT: P 147 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7717 (mp) REVERT: P 269 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.5813 (m-10) REVERT: P 282 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7317 (m-10) REVERT: P 318 LEU cc_start: 0.7426 (pp) cc_final: 0.7164 (tp) outliers start: 19 outliers final: 11 residues processed: 62 average time/residue: 0.7117 time to fit residues: 46.9340 Evaluate side-chains 62 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4490 Z= 0.146 Angle : 0.546 9.592 6122 Z= 0.269 Chirality : 0.042 0.140 693 Planarity : 0.003 0.051 764 Dihedral : 4.737 21.657 597 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.53 % Allowed : 19.50 % Favored : 76.97 % 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: -0.38 (0.35), residues: 547 helix: 1.51 (0.36), residues: 207 sheet: -0.74 (0.43), residues: 140 loop : -1.76 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 297 HIS 0.001 0.000 HIS P 211 PHE 0.010 0.001 PHE A 69 TYR 0.015 0.001 TYR P 134 ARG 0.011 0.000 ARG B 24 *********************** 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 65 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.500 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 106 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7708 (mt) REVERT: B 97 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8544 (p) REVERT: P 134 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7816 (p90) REVERT: P 147 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7694 (mp) REVERT: P 180 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8032 (mp) REVERT: P 269 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.5652 (m-10) REVERT: P 282 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7388 (m-10) outliers start: 17 outliers final: 7 residues processed: 61 average time/residue: 0.7498 time to fit residues: 48.7425 Evaluate side-chains 60 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.0470 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4490 Z= 0.166 Angle : 0.538 8.293 6122 Z= 0.268 Chirality : 0.042 0.140 693 Planarity : 0.003 0.047 764 Dihedral : 4.669 21.167 597 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.73 % Allowed : 20.12 % Favored : 76.14 % 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: -0.25 (0.35), residues: 547 helix: 1.62 (0.36), residues: 207 sheet: -0.60 (0.43), residues: 138 loop : -1.74 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 297 HIS 0.001 0.000 HIS P 211 PHE 0.010 0.001 PHE A 69 TYR 0.016 0.001 TYR P 134 ARG 0.011 0.000 ARG B 24 *********************** 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 67 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 0.416 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 106 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7695 (mt) REVERT: B 79 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7517 (mm110) REVERT: P 134 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7853 (p90) REVERT: P 147 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7685 (mp) REVERT: P 269 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.5713 (m-10) REVERT: P 282 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7397 (m-10) outliers start: 18 outliers final: 10 residues processed: 63 average time/residue: 0.6325 time to fit residues: 42.7595 Evaluate side-chains 64 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 138 TRP Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU 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: 0.5980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 42 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: 0.7959 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4490 Z= 0.206 Angle : 0.559 7.047 6122 Z= 0.277 Chirality : 0.043 0.141 693 Planarity : 0.003 0.042 764 Dihedral : 4.738 21.916 597 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.32 % Allowed : 20.75 % Favored : 75.93 % 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: -0.25 (0.35), residues: 547 helix: 1.62 (0.36), residues: 207 sheet: -0.58 (0.44), residues: 138 loop : -1.75 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 297 HIS 0.001 0.001 HIS P 211 PHE 0.011 0.001 PHE A 69 TYR 0.017 0.001 TYR P 134 ARG 0.009 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 49 time to evaluate : 0.477 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 106 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7796 (mt) REVERT: B 79 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7697 (mm-40) REVERT: P 134 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7893 (p90) REVERT: P 147 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7705 (mp) REVERT: P 269 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.5810 (m-10) REVERT: P 282 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7327 (m-10) outliers start: 16 outliers final: 9 residues processed: 63 average time/residue: 0.6424 time to fit residues: 43.4518 Evaluate side-chains 62 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU 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: 0.5980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4490 Z= 0.246 Angle : 0.568 7.443 6122 Z= 0.287 Chirality : 0.044 0.142 693 Planarity : 0.004 0.040 764 Dihedral : 4.887 22.760 597 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.11 % Allowed : 20.95 % Favored : 75.93 % 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 (0.35), residues: 547 helix: 1.54 (0.36), residues: 207 sheet: -0.59 (0.44), residues: 138 loop : -1.77 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 297 HIS 0.002 0.001 HIS B 55 PHE 0.013 0.001 PHE A 69 TYR 0.019 0.001 TYR P 134 ARG 0.008 0.000 ARG B 24 ********************** 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: 15 poor density : 50 time to evaluate : 0.470 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 106 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7828 (mt) REVERT: B 79 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7682 (mm-40) REVERT: P 147 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7739 (mp) REVERT: P 269 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.5910 (m-10) REVERT: P 282 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7311 (m-10) outliers start: 15 outliers final: 9 residues processed: 63 average time/residue: 0.7259 time to fit residues: 48.9416 Evaluate side-chains 63 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0270 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 34 optimal weight: 0.0050 overall best weight: 0.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.160458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127867 restraints weight = 4874.097| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.01 r_work: 0.3338 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4490 Z= 0.153 Angle : 0.533 7.442 6122 Z= 0.265 Chirality : 0.042 0.142 693 Planarity : 0.003 0.037 764 Dihedral : 4.644 21.197 597 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.11 % Allowed : 21.37 % Favored : 75.52 % 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 (0.36), residues: 547 helix: 1.76 (0.36), residues: 207 sheet: -0.46 (0.44), residues: 138 loop : -1.67 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 297 HIS 0.001 0.000 HIS P 211 PHE 0.009 0.001 PHE A 69 TYR 0.015 0.001 TYR P 134 ARG 0.008 0.000 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1706.51 seconds wall clock time: 30 minutes 29.25 seconds (1829.25 seconds total)