Starting phenix.real_space_refine on Fri Aug 2 13:23:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/08_2024/8k5d_36902.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/08_2024/8k5d_36902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/08_2024/8k5d_36902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/08_2024/8k5d_36902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/08_2024/8k5d_36902.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/08_2024/8k5d_36902.cif" } resolution = 3.74 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= -0.001 sd= 0.031 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: 5 Type Number sf(0) Gaussians S 17 5.16 5 Cl 1 4.86 5 C 1561 2.51 5 N 394 2.21 5 O 372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 37": "OE1" <-> "OE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2345 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2328 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'OKL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.11, per 1000 atoms: 0.90 Number of scatterers: 2345 At special positions: 0 Unit cell: (69.72, 62.25, 79.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 17 16.00 O 372 8.00 N 394 7.00 C 1561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " 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: 0.94 Conformation dependent library (CDL) restraints added in 436.2 milliseconds 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 558 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 75.9% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.068A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 89 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 130 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 166 removed outlier: 5.124A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.816A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 260 removed outlier: 3.717A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.597A pdb=" N ARG A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 165 hydrogen bonds defined for protein. 483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 713 1.34 - 1.46: 438 1.46 - 1.58: 1236 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 2413 Sorted by residual: bond pdb=" C07 OKL A 401 " pdb=" O08 OKL A 401 " ideal model delta sigma weight residual 1.214 1.398 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C10 OKL A 401 " pdb=" O11 OKL A 401 " ideal model delta sigma weight residual 1.215 1.396 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" C15 OKL A 401 " pdb="CL17 OKL A 401 " ideal model delta sigma weight residual 1.692 1.784 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C10 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 1.390 1.325 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C07 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 1.384 1.328 0.056 2.00e-02 2.50e+03 7.72e+00 ... (remaining 2408 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.35: 85 107.35 - 114.21: 1396 114.21 - 121.06: 1214 121.06 - 127.92: 555 127.92 - 134.77: 34 Bond angle restraints: 3284 Sorted by residual: angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 111.91 108.72 3.19 8.90e-01 1.26e+00 1.28e+01 angle pdb=" N PRO A 31 " pdb=" CA PRO A 31 " pdb=" C PRO A 31 " ideal model delta sigma weight residual 110.70 114.65 -3.95 1.22e+00 6.72e-01 1.05e+01 angle pdb=" CA PRO A 31 " pdb=" C PRO A 31 " pdb=" N PRO A 32 " ideal model delta sigma weight residual 117.93 121.72 -3.79 1.20e+00 6.94e-01 9.98e+00 angle pdb=" C07 OKL A 401 " pdb=" N09 OKL A 401 " pdb=" C10 OKL A 401 " ideal model delta sigma weight residual 129.77 120.31 9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" C12 OKL A 401 " pdb=" C10 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 109.84 119.23 -9.39 3.00e+00 1.11e-01 9.80e+00 ... (remaining 3279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.19: 1261 27.19 - 54.38: 120 54.38 - 81.58: 7 81.58 - 108.77: 0 108.77 - 135.96: 1 Dihedral angle restraints: 1389 sinusoidal: 535 harmonic: 854 Sorted by residual: dihedral pdb=" C03 OKL A 401 " pdb=" C04 OKL A 401 " pdb=" C05 OKL A 401 " pdb=" N06 OKL A 401 " ideal model delta sinusoidal sigma weight residual 183.45 47.49 135.96 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" CA LYS A 164 " pdb=" C LYS A 164 " pdb=" N LYS A 165 " pdb=" CA LYS A 165 " ideal model delta harmonic sigma weight residual -180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLU A 196 " pdb=" C GLU A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual 180.00 163.64 16.36 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 1386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 261 0.037 - 0.074: 82 0.074 - 0.110: 28 0.110 - 0.147: 4 0.147 - 0.184: 3 Chirality restraints: 378 Sorted by residual: chirality pdb=" CA ASN A 110 " pdb=" N ASN A 110 " pdb=" C ASN A 110 " pdb=" CB ASN A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA PRO A 31 " pdb=" N PRO A 31 " pdb=" C PRO A 31 " pdb=" CB PRO A 31 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA THR A 159 " pdb=" N THR A 159 " pdb=" C THR A 159 " pdb=" CB THR A 159 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 375 not shown) Planarity restraints: 398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 167 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 168 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 31 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 32 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 131 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 132 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.022 5.00e-02 4.00e+02 ... (remaining 395 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 258 2.74 - 3.28: 2460 3.28 - 3.82: 3903 3.82 - 4.36: 4195 4.36 - 4.90: 7307 Nonbonded interactions: 18123 Sorted by model distance: nonbonded pdb=" O ILE A 278 " pdb=" OG SER A 281 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASN A 68 " pdb=" NE1 TRP A 152 " model vdw 2.322 3.120 nonbonded pdb=" N SER A 179 " pdb=" O08 OKL A 401 " model vdw 2.326 3.120 nonbonded pdb=" NH2 ARG A 111 " pdb=" O11 OKL A 401 " model vdw 2.330 3.120 nonbonded pdb=" N ASP A 221 " pdb=" OD1 ASP A 221 " model vdw 2.345 3.120 ... (remaining 18118 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 group one per residue 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.970 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.007 0.184 2413 Z= 0.474 Angle : 0.756 9.520 3284 Z= 0.371 Chirality : 0.043 0.184 378 Planarity : 0.005 0.045 398 Dihedral : 19.082 135.960 825 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.40 % Allowed : 41.70 % Favored : 57.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.51), residues: 289 helix: 1.39 (0.37), residues: 202 sheet: None (None), residues: 0 loop : -2.40 (0.68), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 93 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.005 0.001 TYR A 126 ARG 0.002 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.4006 (OUTLIER) cc_final: 0.3713 (m-10) REVERT: A 103 MET cc_start: 0.7450 (tpp) cc_final: 0.7040 (tpp) REVERT: A 170 GLN cc_start: 0.8195 (tp40) cc_final: 0.7866 (tp40) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.0810 time to fit residues: 7.1688 Evaluate side-chains 68 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2413 Z= 0.199 Angle : 0.575 7.455 3284 Z= 0.298 Chirality : 0.040 0.130 378 Planarity : 0.005 0.049 398 Dihedral : 9.546 141.589 319 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.26 % Allowed : 34.41 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.50), residues: 289 helix: 1.25 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.68 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE A 197 TYR 0.007 0.001 TYR A 284 ARG 0.001 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8577 (m-30) cc_final: 0.8284 (m-30) outliers start: 13 outliers final: 11 residues processed: 75 average time/residue: 0.0926 time to fit residues: 8.8379 Evaluate side-chains 78 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7262 ------------------------------------------------------------------------------- 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: 0.7798 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2413 Z= 0.253 Angle : 0.595 8.054 3284 Z= 0.304 Chirality : 0.040 0.132 378 Planarity : 0.005 0.049 398 Dihedral : 9.169 142.198 317 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 7.69 % Allowed : 32.79 % Favored : 59.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.51), residues: 289 helix: 1.32 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.61 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 197 TYR 0.009 0.002 TYR A 284 ARG 0.002 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 87 TYR cc_start: 0.8492 (m-80) cc_final: 0.8271 (m-80) REVERT: A 290 ASP cc_start: 0.8671 (m-30) cc_final: 0.8189 (m-30) outliers start: 19 outliers final: 13 residues processed: 77 average time/residue: 0.1110 time to fit residues: 10.6210 Evaluate side-chains 81 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 28 optimal weight: 0.0040 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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: 0.7787 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2413 Z= 0.218 Angle : 0.592 6.958 3284 Z= 0.300 Chirality : 0.040 0.123 378 Planarity : 0.005 0.048 398 Dihedral : 9.082 140.922 317 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.07 % Allowed : 33.60 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.51), residues: 289 helix: 1.46 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.64 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.007 0.001 TYR A 284 ARG 0.001 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8486 (ttp-110) cc_final: 0.8261 (ttm-80) REVERT: A 87 TYR cc_start: 0.8494 (m-80) cc_final: 0.8190 (m-80) REVERT: A 290 ASP cc_start: 0.8683 (m-30) cc_final: 0.8057 (m-30) outliers start: 15 outliers final: 12 residues processed: 75 average time/residue: 0.1009 time to fit residues: 9.4361 Evaluate side-chains 79 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7799 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2413 Z= 0.232 Angle : 0.597 8.678 3284 Z= 0.302 Chirality : 0.040 0.141 378 Planarity : 0.005 0.049 398 Dihedral : 9.116 141.656 317 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 8.91 % Allowed : 32.79 % Favored : 58.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.51), residues: 289 helix: 1.42 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.56 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.008 0.001 TYR A 126 ARG 0.001 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3829 (OUTLIER) cc_final: 0.3604 (m-10) REVERT: A 63 ARG cc_start: 0.8484 (ttp-110) cc_final: 0.8215 (ttm-80) REVERT: A 110 ASN cc_start: 0.8673 (m-40) cc_final: 0.8470 (m110) REVERT: A 290 ASP cc_start: 0.8682 (m-30) cc_final: 0.8333 (m-30) outliers start: 22 outliers final: 20 residues processed: 78 average time/residue: 0.1095 time to fit residues: 10.5590 Evaluate side-chains 87 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2413 Z= 0.243 Angle : 0.600 7.781 3284 Z= 0.310 Chirality : 0.041 0.155 378 Planarity : 0.005 0.049 398 Dihedral : 9.140 142.145 317 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 9.31 % Allowed : 31.58 % Favored : 59.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.51), residues: 289 helix: 1.43 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.60 (0.68), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 197 TYR 0.008 0.001 TYR A 126 ARG 0.001 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 68 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3845 (OUTLIER) cc_final: 0.3617 (m-10) REVERT: A 63 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8202 (ttm-80) REVERT: A 103 MET cc_start: 0.7540 (tpp) cc_final: 0.7325 (tpp) REVERT: A 110 ASN cc_start: 0.8690 (m-40) cc_final: 0.8471 (m110) REVERT: A 290 ASP cc_start: 0.8690 (m-30) cc_final: 0.8298 (m-30) outliers start: 23 outliers final: 17 residues processed: 80 average time/residue: 0.1035 time to fit residues: 10.2394 Evaluate side-chains 86 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2413 Z= 0.255 Angle : 0.608 7.216 3284 Z= 0.313 Chirality : 0.041 0.135 378 Planarity : 0.005 0.050 398 Dihedral : 9.204 142.695 317 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.91 % Allowed : 32.39 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.51), residues: 289 helix: 1.42 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.71 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 197 TYR 0.009 0.001 TYR A 126 ARG 0.001 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3841 (OUTLIER) cc_final: 0.3611 (m-10) REVERT: A 63 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.8197 (ttm-80) REVERT: A 103 MET cc_start: 0.7315 (tpp) cc_final: 0.7107 (tpp) REVERT: A 290 ASP cc_start: 0.8749 (m-30) cc_final: 0.8341 (m-30) outliers start: 22 outliers final: 18 residues processed: 78 average time/residue: 0.1126 time to fit residues: 10.9110 Evaluate side-chains 85 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2413 Z= 0.259 Angle : 0.631 8.874 3284 Z= 0.320 Chirality : 0.042 0.165 378 Planarity : 0.005 0.048 398 Dihedral : 9.188 142.097 317 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.91 % Allowed : 32.39 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.51), residues: 289 helix: 1.56 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.09 (0.63), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.002 0.001 HIS A 184 PHE 0.010 0.001 PHE A 197 TYR 0.009 0.001 TYR A 126 ARG 0.002 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3843 (OUTLIER) cc_final: 0.3613 (m-10) REVERT: A 63 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8196 (ttm-80) REVERT: A 190 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8952 (mm-30) REVERT: A 290 ASP cc_start: 0.8743 (m-30) cc_final: 0.8319 (m-30) outliers start: 22 outliers final: 18 residues processed: 78 average time/residue: 0.1154 time to fit residues: 11.2425 Evaluate side-chains 86 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2413 Z= 0.243 Angle : 0.642 8.763 3284 Z= 0.322 Chirality : 0.041 0.180 378 Planarity : 0.005 0.048 398 Dihedral : 9.156 141.263 317 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 7.69 % Allowed : 33.60 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.51), residues: 289 helix: 1.54 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.11 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.001 0.000 HIS A 184 PHE 0.010 0.001 PHE A 197 TYR 0.008 0.001 TYR A 126 ARG 0.002 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3839 (OUTLIER) cc_final: 0.3551 (m-10) REVERT: A 103 MET cc_start: 0.7489 (tpp) cc_final: 0.7253 (tpp) REVERT: A 290 ASP cc_start: 0.8731 (m-30) cc_final: 0.8297 (m-30) outliers start: 19 outliers final: 18 residues processed: 77 average time/residue: 0.1050 time to fit residues: 9.9630 Evaluate side-chains 85 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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: 0.7796 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2413 Z= 0.205 Angle : 0.631 8.766 3284 Z= 0.317 Chirality : 0.041 0.182 378 Planarity : 0.005 0.049 398 Dihedral : 9.069 139.811 317 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 7.69 % Allowed : 32.79 % Favored : 59.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.51), residues: 289 helix: 1.38 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.83 (0.65), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.001 0.000 HIS A 189 PHE 0.011 0.001 PHE A 54 TYR 0.006 0.001 TYR A 126 ARG 0.002 0.000 ARG A 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8186 (ttm110) REVERT: A 103 MET cc_start: 0.7516 (tpp) cc_final: 0.7290 (tpp) REVERT: A 137 ASN cc_start: 0.8326 (m-40) cc_final: 0.7887 (m-40) REVERT: A 190 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8957 (mm-30) REVERT: A 290 ASP cc_start: 0.8714 (m-30) cc_final: 0.8280 (m-30) outliers start: 19 outliers final: 16 residues processed: 79 average time/residue: 0.1021 time to fit residues: 10.0138 Evaluate side-chains 84 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138351 restraints weight = 3861.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141368 restraints weight = 2281.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143678 restraints weight = 1578.668| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2413 Z= 0.187 Angle : 0.612 8.797 3284 Z= 0.306 Chirality : 0.040 0.187 378 Planarity : 0.005 0.050 398 Dihedral : 8.825 136.300 317 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.26 % Allowed : 35.63 % Favored : 59.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.51), residues: 289 helix: 1.48 (0.37), residues: 214 sheet: None (None), residues: 0 loop : -2.84 (0.65), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 91 HIS 0.002 0.000 HIS A 161 PHE 0.013 0.001 PHE A 197 TYR 0.004 0.001 TYR A 126 ARG 0.003 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 890.86 seconds wall clock time: 16 minutes 26.49 seconds (986.49 seconds total)