Starting phenix.real_space_refine on Sun Mar 10 14:49:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/03_2024/8k5d_36902_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/03_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_36902/03_2024/8k5d_36902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/03_2024/8k5d_36902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/03_2024/8k5d_36902_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5d_36902/03_2024/8k5d_36902_updated.pdb" } 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-5265/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: 1.95, per 1000 atoms: 0.83 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: 1.06 Conformation dependent library (CDL) restraints added in 457.3 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... running ksdssp... Secondary structure from input PDB file: 8 helices and 2 sheets defined 70.4% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 30 through 53 removed outlier: 4.068A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 88 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 98 through 129 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 141 through 165 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) Processing helix chain 'A' and resid 188 through 217 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 224 through 259 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 267 through 293 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= A, first strand: chain 'A' and resid 10 through 12 Processing sheet with id= B, first strand: chain 'A' and resid 169 through 171 153 hydrogen bonds defined for protein. 453 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: 0.58 Time building geometry restraints manager: 1.15 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: 259 2.74 - 3.28: 2468 3.28 - 3.82: 3913 3.82 - 4.36: 4220 4.36 - 4.90: 7311 Nonbonded interactions: 18171 Sorted by model distance: nonbonded pdb=" O ILE A 278 " pdb=" OG SER A 281 " model vdw 2.203 2.440 nonbonded pdb=" OD1 ASN A 68 " pdb=" NE1 TRP A 152 " model vdw 2.322 2.520 nonbonded pdb=" N SER A 179 " pdb=" O08 OKL A 401 " model vdw 2.326 2.520 nonbonded pdb=" NH2 ARG A 111 " pdb=" O11 OKL A 401 " model vdw 2.330 2.520 nonbonded pdb=" N ASP A 221 " pdb=" OD1 ASP A 221 " model vdw 2.345 2.520 ... (remaining 18166 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: 0.400 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: 1.780 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.610 Find NCS groups from input model: 0.070 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- 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= 0.503 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 : 0.285 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: 0.0955 time to fit residues: 8.4008 Evaluate side-chains 68 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.0623 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= 0.243 Angle : 0.582 7.335 3284 Z= 0.300 Chirality : 0.040 0.140 378 Planarity : 0.005 0.047 398 Dihedral : 9.862 147.377 319 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.88 % Allowed : 33.60 % 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: 0.31 (0.50), residues: 289 helix: 1.43 (0.36), residues: 207 sheet: None (None), residues: 0 loop : -3.17 (0.61), residues: 82 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 0.009 0.001 PHE A 197 TYR 0.009 0.002 TYR A 87 ARG 0.002 0.000 ARG A 251 *********************** 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 84 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 87 TYR cc_start: 0.8566 (m-80) cc_final: 0.8312 (m-80) REVERT: A 103 MET cc_start: 0.7547 (tpp) cc_final: 0.7338 (tpp) REVERT: A 170 GLN cc_start: 0.8192 (tp40) cc_final: 0.7956 (tp-100) REVERT: A 290 ASP cc_start: 0.8717 (m-30) cc_final: 0.8467 (m-30) outliers start: 17 outliers final: 13 residues processed: 76 average time/residue: 0.1060 time to fit residues: 9.9352 Evaluate side-chains 78 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 20 VAL 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 165 LYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 260 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: 0.9980 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2413 Z= 0.188 Angle : 0.553 8.505 3284 Z= 0.279 Chirality : 0.039 0.134 378 Planarity : 0.005 0.049 398 Dihedral : 9.251 144.957 317 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.48 % Allowed : 34.41 % 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 (0.50), residues: 289 helix: 1.50 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -2.84 (0.62), residues: 76 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 0.011 0.001 PHE A 197 TYR 0.006 0.001 TYR A 284 ARG 0.001 0.000 ARG A 218 *********************** 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 82 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3807 (OUTLIER) cc_final: 0.3500 (m-10) REVERT: A 87 TYR cc_start: 0.8478 (m-80) cc_final: 0.8032 (m-80) REVERT: A 170 GLN cc_start: 0.8176 (tp40) cc_final: 0.7963 (tp40) REVERT: A 290 ASP cc_start: 0.8744 (m-30) cc_final: 0.8284 (m-30) outliers start: 16 outliers final: 7 residues processed: 75 average time/residue: 0.0882 time to fit residues: 8.5481 Evaluate side-chains 72 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 274 LEU 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: 0.3980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 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: 0.7813 moved from start: 0.0984 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= 0.231 Angle : 0.565 8.370 3284 Z= 0.284 Chirality : 0.039 0.124 378 Planarity : 0.005 0.051 398 Dihedral : 9.292 145.945 317 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 8.50 % Allowed : 31.98 % 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: 0.69 (0.51), residues: 289 helix: 1.69 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -2.99 (0.62), residues: 81 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 0.009 0.001 PHE A 197 TYR 0.008 0.002 TYR A 126 ARG 0.002 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: 21 poor density : 63 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3846 (OUTLIER) cc_final: 0.3572 (m-10) REVERT: A 110 ASN cc_start: 0.8382 (m-40) cc_final: 0.7996 (m110) REVERT: A 165 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7325 (pttt) REVERT: A 170 GLN cc_start: 0.8215 (tp40) cc_final: 0.7974 (tp40) REVERT: A 290 ASP cc_start: 0.8749 (m-30) cc_final: 0.8144 (m-30) outliers start: 21 outliers final: 15 residues processed: 76 average time/residue: 0.0883 time to fit residues: 8.5219 Evaluate side-chains 80 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 51 ILE 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 221 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 274 LEU 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: 0.6980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.7886 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 2413 Z= 0.361 Angle : 0.632 7.060 3284 Z= 0.323 Chirality : 0.042 0.142 378 Planarity : 0.005 0.048 398 Dihedral : 9.576 148.755 317 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % 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: 0.36 (0.50), residues: 289 helix: 1.42 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.06 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 152 HIS 0.003 0.001 HIS A 131 PHE 0.010 0.001 PHE A 206 TYR 0.013 0.002 TYR A 87 ARG 0.003 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 90 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3949 (OUTLIER) cc_final: 0.3669 (m-10) REVERT: A 170 GLN cc_start: 0.8431 (tp40) cc_final: 0.8161 (tp40) REVERT: A 282 PHE cc_start: 0.8436 (m-80) cc_final: 0.8167 (t80) REVERT: A 290 ASP cc_start: 0.8846 (m-30) cc_final: 0.8289 (m-30) outliers start: 23 outliers final: 21 residues processed: 80 average time/residue: 0.1186 time to fit residues: 11.4749 Evaluate side-chains 88 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 17 ASN 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 51 ILE 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 176 LEU Chi-restraints excluded: chain A residue 221 ASP 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 285 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2413 Z= 0.201 Angle : 0.601 9.020 3284 Z= 0.304 Chirality : 0.040 0.157 378 Planarity : 0.004 0.050 398 Dihedral : 9.375 146.667 317 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 7.69 % Allowed : 34.01 % 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: 0.59 (0.50), residues: 289 helix: 1.60 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.02 (0.61), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 93 HIS 0.002 0.001 HIS A 131 PHE 0.010 0.001 PHE A 197 TYR 0.006 0.001 TYR A 87 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 87 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3851 (OUTLIER) cc_final: 0.3577 (m-10) REVERT: A 63 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.8201 (ttm-80) REVERT: A 110 ASN cc_start: 0.8468 (m-40) cc_final: 0.8148 (m110) REVERT: A 282 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.8133 (t80) REVERT: A 290 ASP cc_start: 0.8846 (m-30) cc_final: 0.8238 (m-30) outliers start: 19 outliers final: 15 residues processed: 81 average time/residue: 0.1052 time to fit residues: 10.5250 Evaluate side-chains 82 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 17 ASN 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 51 ILE 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 176 LEU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 282 PHE 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: 2.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7871 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 2413 Z= 0.310 Angle : 0.653 8.589 3284 Z= 0.329 Chirality : 0.042 0.150 378 Planarity : 0.005 0.050 398 Dihedral : 9.501 147.919 317 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 8.50 % Allowed : 34.41 % Favored : 57.09 % 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: 0.36 (0.50), residues: 289 helix: 1.44 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.12 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 50 HIS 0.002 0.001 HIS A 131 PHE 0.010 0.001 PHE A 54 TYR 0.011 0.002 TYR A 126 ARG 0.003 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 87 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3824 (OUTLIER) cc_final: 0.3525 (m-10) REVERT: A 290 ASP cc_start: 0.8873 (m-30) cc_final: 0.8528 (m-30) outliers start: 21 outliers final: 18 residues processed: 78 average time/residue: 0.1165 time to fit residues: 11.0413 Evaluate side-chains 86 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 17 ASN 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 51 ILE 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 176 LEU Chi-restraints excluded: chain A residue 221 ASP 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 274 LEU Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7852 moved from start: 0.1433 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= 0.252 Angle : 0.624 8.464 3284 Z= 0.316 Chirality : 0.041 0.161 378 Planarity : 0.005 0.051 398 Dihedral : 9.420 146.738 317 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 7.29 % Allowed : 35.63 % Favored : 57.09 % 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: 0.39 (0.50), residues: 289 helix: 1.49 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.18 (0.60), residues: 81 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 0.010 0.001 PHE A 54 TYR 0.008 0.002 TYR A 126 ARG 0.002 0.000 ARG A 251 *********************** 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 84 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3930 (OUTLIER) cc_final: 0.3695 (m-10) REVERT: A 110 ASN cc_start: 0.8396 (m-40) cc_final: 0.8133 (m110) REVERT: A 290 ASP cc_start: 0.8831 (m-30) cc_final: 0.8458 (m-30) outliers start: 18 outliers final: 16 residues processed: 78 average time/residue: 0.1404 time to fit residues: 13.3206 Evaluate side-chains 81 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 17 ASN 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 51 ILE 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 176 LEU Chi-restraints excluded: chain A residue 221 ASP 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 274 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2413 Z= 0.196 Angle : 0.596 8.393 3284 Z= 0.300 Chirality : 0.040 0.151 378 Planarity : 0.005 0.053 398 Dihedral : 9.294 145.550 317 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 6.88 % Allowed : 36.44 % Favored : 56.68 % 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: 0.59 (0.50), residues: 289 helix: 1.67 (0.36), residues: 207 sheet: None (None), residues: 0 loop : -3.15 (0.60), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 91 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE A 54 TYR 0.005 0.001 TYR A 87 ARG 0.001 0.000 ARG A 125 *********************** 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 84 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7962 (mt-10) REVERT: A 59 TRP cc_start: 0.3730 (OUTLIER) cc_final: 0.3496 (m-10) REVERT: A 63 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.8163 (ttm110) REVERT: A 290 ASP cc_start: 0.8748 (m-30) cc_final: 0.8352 (m-30) outliers start: 17 outliers final: 15 residues processed: 79 average time/residue: 0.1111 time to fit residues: 10.7436 Evaluate side-chains 78 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 17 ASN 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 176 LEU Chi-restraints excluded: chain A residue 221 ASP 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 274 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 26 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 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2413 Z= 0.205 Angle : 0.598 8.154 3284 Z= 0.301 Chirality : 0.041 0.150 378 Planarity : 0.005 0.054 398 Dihedral : 9.286 145.536 317 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.48 % Allowed : 37.25 % Favored : 56.28 % 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: 0.57 (0.50), residues: 289 helix: 1.64 (0.36), residues: 207 sheet: None (None), residues: 0 loop : -3.14 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.003 0.001 HIS A 161 PHE 0.012 0.001 PHE A 54 TYR 0.006 0.001 TYR A 126 ARG 0.001 0.000 ARG A 125 ********************** 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 82 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3849 (OUTLIER) cc_final: 0.3546 (m-10) REVERT: A 161 HIS cc_start: 0.7705 (p90) cc_final: 0.7163 (p90) REVERT: A 290 ASP cc_start: 0.8740 (m-30) cc_final: 0.8324 (m-30) outliers start: 16 outliers final: 14 residues processed: 77 average time/residue: 0.1143 time to fit residues: 10.7758 Evaluate side-chains 80 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 17 ASN 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 221 ASP 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 274 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** 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 = 0.3748 r_free = 0.3748 target = 0.152114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134571 restraints weight = 3901.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137617 restraints weight = 2346.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139678 restraints weight = 1622.151| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2413 Z= 0.205 Angle : 0.597 8.129 3284 Z= 0.300 Chirality : 0.041 0.149 378 Planarity : 0.005 0.054 398 Dihedral : 9.254 144.984 317 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.07 % Allowed : 37.25 % Favored : 56.68 % 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: 0.57 (0.50), residues: 289 helix: 1.65 (0.36), residues: 207 sheet: None (None), residues: 0 loop : -3.15 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 152 HIS 0.003 0.001 HIS A 161 PHE 0.012 0.001 PHE A 54 TYR 0.006 0.001 TYR A 87 ARG 0.001 0.000 ARG A 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 921.33 seconds wall clock time: 17 minutes 17.16 seconds (1037.16 seconds total)