Starting phenix.real_space_refine on Thu Jul 18 18:44:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/07_2024/8tte_41605.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/07_2024/8tte_41605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/07_2024/8tte_41605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/07_2024/8tte_41605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/07_2024/8tte_41605.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/07_2024/8tte_41605.cif" } resolution = 3.26 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= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2015 2.51 5 N 454 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2991 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2842 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 149 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 13} Time building chain proxies: 2.61, per 1000 atoms: 0.87 Number of scatterers: 2991 At special positions: 0 Unit cell: (55.704, 73.428, 75.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 504 8.00 N 454 7.00 C 2015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.24 Conformation dependent library (CDL) restraints added in 691.6 milliseconds 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 694 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 88.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 3.549A pdb=" N ILE A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.748A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 66 removed outlier: 3.576A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 67 through 86 removed outlier: 3.631A pdb=" N ALA A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 120 removed outlier: 3.705A pdb=" N LEU A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 125 removed outlier: 4.070A pdb=" N LYS A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 148 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 157 through 177 Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.994A pdb=" N LYS A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 199' Processing helix chain 'A' and resid 204 through 233 removed outlier: 4.006A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 264 removed outlier: 5.726A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.732A pdb=" N SER A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.844A pdb=" N ALA A 312 " --> pdb=" O MET A 308 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.804A pdb=" N ALA A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 3.736A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 382 Processing sheet with id=AA1, first strand: chain 'C' and resid 129 through 132 245 hydrogen bonds defined for protein. 723 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: 0.65 Time building geometry restraints manager: 1.27 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: 858 1.34 - 1.46: 650 1.46 - 1.58: 1530 1.58 - 1.70: 0 1.70 - 1.82: 35 Bond restraints: 3073 Sorted by residual: bond pdb=" CE1 HIS A 123 " pdb=" NE2 HIS A 123 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" N VAL A 365 " pdb=" CA VAL A 365 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.13e+00 bond pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.20e-02 6.94e+03 7.98e+00 bond pdb=" N VAL A 302 " pdb=" CA VAL A 302 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.95e+00 bond pdb=" N ILE A 199 " pdb=" CA ILE A 199 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 7.89e+00 ... (remaining 3068 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.58: 55 104.58 - 111.99: 1483 111.99 - 119.39: 1057 119.39 - 126.80: 1533 126.80 - 134.20: 39 Bond angle restraints: 4167 Sorted by residual: angle pdb=" N LEU A 17 " pdb=" CA LEU A 17 " pdb=" C LEU A 17 " ideal model delta sigma weight residual 111.69 105.40 6.29 1.23e+00 6.61e-01 2.62e+01 angle pdb=" CB MET A 361 " pdb=" CG MET A 361 " pdb=" SD MET A 361 " ideal model delta sigma weight residual 112.70 122.21 -9.51 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET A 263 " pdb=" CG MET A 263 " pdb=" SD MET A 263 " ideal model delta sigma weight residual 112.70 103.36 9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" N MET A 157 " pdb=" CA MET A 157 " pdb=" C MET A 157 " ideal model delta sigma weight residual 109.81 116.65 -6.84 2.21e+00 2.05e-01 9.57e+00 angle pdb=" N PHE A 262 " pdb=" CA PHE A 262 " pdb=" CB PHE A 262 " ideal model delta sigma weight residual 110.30 114.90 -4.60 1.54e+00 4.22e-01 8.94e+00 ... (remaining 4162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 1476 16.16 - 32.32: 202 32.32 - 48.48: 59 48.48 - 64.64: 12 64.64 - 80.80: 2 Dihedral angle restraints: 1751 sinusoidal: 658 harmonic: 1093 Sorted by residual: dihedral pdb=" CA TRP C 131 " pdb=" C TRP C 131 " pdb=" N TYR C 132 " pdb=" CA TYR C 132 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" N MET A 157 " pdb=" CA MET A 157 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR A 235 " pdb=" C TYR A 235 " pdb=" N SER A 236 " pdb=" CA SER A 236 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 321 0.047 - 0.095: 100 0.095 - 0.142: 42 0.142 - 0.189: 12 0.189 - 0.237: 4 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA LEU A 17 " pdb=" N LEU A 17 " pdb=" C LEU A 17 " pdb=" CB LEU A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE A 12 " pdb=" N ILE A 12 " pdb=" C ILE A 12 " pdb=" CB ILE A 12 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 476 not shown) Planarity restraints: 506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 262 " 0.021 2.00e-02 2.50e+03 2.30e-02 9.29e+00 pdb=" CG PHE A 262 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 262 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 262 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 262 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 262 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 262 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 157 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" C MET A 157 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A 157 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO A 158 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 233 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C VAL A 233 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL A 233 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 234 " 0.008 2.00e-02 2.50e+03 ... (remaining 503 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 891 2.82 - 3.34: 3284 3.34 - 3.86: 5129 3.86 - 4.38: 5547 4.38 - 4.90: 9715 Nonbonded interactions: 24566 Sorted by model distance: nonbonded pdb=" OG SER A 236 " pdb=" OD1 ASP A 239 " model vdw 2.301 2.440 nonbonded pdb=" NZ LYS A 68 " pdb=" O ILE A 177 " model vdw 2.365 2.520 nonbonded pdb=" OG1 THR A 36 " pdb=" OD1 ASP A 352 " model vdw 2.396 2.440 nonbonded pdb=" N SER A 38 " pdb=" OD2 ASP A 352 " model vdw 2.404 2.520 nonbonded pdb=" O LEU A 276 " pdb=" OG SER A 279 " model vdw 2.476 2.440 ... (remaining 24561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.190 Find NCS groups from input model: 0.030 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.006 0.041 3073 Z= 0.374 Angle : 0.915 9.513 4167 Z= 0.632 Chirality : 0.059 0.237 479 Planarity : 0.004 0.030 506 Dihedral : 16.553 80.796 1057 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.94 % Allowed : 28.53 % Favored : 70.53 % 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: 0.55 (0.44), residues: 379 helix: 1.04 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -2.71 (0.73), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.053 0.002 PHE A 262 TYR 0.019 0.001 TYR A 278 ARG 0.002 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.341 Fit side-chains REVERT: A 156 ARG cc_start: 0.6732 (mtm180) cc_final: 0.5692 (mtp85) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.1408 time to fit residues: 12.1852 Evaluate side-chains 66 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.0010 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.0070 chunk 10 optimal weight: 0.5980 overall best weight: 0.4404 ------------------------------------------------------------------------------- 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: 0.7786 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3073 Z= 0.196 Angle : 0.649 6.933 4167 Z= 0.334 Chirality : 0.041 0.174 479 Planarity : 0.004 0.026 506 Dihedral : 4.575 19.102 407 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.70 % Allowed : 28.21 % Favored : 67.08 % 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: 1.86 (0.46), residues: 379 helix: 1.91 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.41 (0.86), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 201 HIS 0.004 0.001 HIS A 379 PHE 0.038 0.002 PHE A 262 TYR 0.017 0.001 TYR A 278 ARG 0.002 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 235 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.7057 (m-10) outliers start: 15 outliers final: 6 residues processed: 75 average time/residue: 0.1305 time to fit residues: 12.1935 Evaluate side-chains 70 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 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: 0.7819 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3073 Z= 0.215 Angle : 0.666 8.264 4167 Z= 0.338 Chirality : 0.041 0.162 479 Planarity : 0.004 0.026 506 Dihedral : 4.477 18.688 405 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.39 % Allowed : 30.41 % Favored : 65.20 % 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: 2.00 (0.47), residues: 379 helix: 2.00 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.23 (0.90), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.012 0.001 PHE A 16 TYR 0.015 0.001 TYR A 278 ARG 0.002 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.265 Fit side-chains REVERT: A 51 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7307 (tp40) REVERT: A 76 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8618 (mm) REVERT: A 150 MET cc_start: 0.7210 (pmm) cc_final: 0.6781 (pmm) REVERT: A 165 LEU cc_start: 0.8591 (tp) cc_final: 0.8387 (tp) REVERT: A 235 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7148 (m-10) outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 0.1291 time to fit residues: 12.6220 Evaluate side-chains 76 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 36 optimal weight: 0.3980 chunk 18 optimal weight: 0.0070 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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: 0.7786 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3073 Z= 0.187 Angle : 0.641 6.802 4167 Z= 0.327 Chirality : 0.040 0.158 479 Planarity : 0.004 0.027 506 Dihedral : 4.350 19.161 405 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.70 % Allowed : 30.09 % Favored : 65.20 % 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: 2.12 (0.47), residues: 379 helix: 2.06 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.14 (0.94), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.004 0.001 HIS A 379 PHE 0.050 0.002 PHE A 262 TYR 0.015 0.001 TYR A 278 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.322 Fit side-chains REVERT: A 51 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7274 (tp40) REVERT: A 150 MET cc_start: 0.7119 (pmm) cc_final: 0.6682 (pmm) REVERT: A 235 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7112 (m-10) outliers start: 15 outliers final: 11 residues processed: 80 average time/residue: 0.1238 time to fit residues: 12.3359 Evaluate side-chains 79 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3073 Z= 0.198 Angle : 0.669 10.853 4167 Z= 0.335 Chirality : 0.041 0.159 479 Planarity : 0.004 0.029 506 Dihedral : 4.310 19.363 405 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.58 % Allowed : 28.84 % Favored : 64.58 % 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: 2.12 (0.47), residues: 379 helix: 2.07 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.13 (0.93), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.012 0.001 PHE A 16 TYR 0.013 0.001 TYR A 278 ARG 0.002 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.340 Fit side-chains REVERT: A 51 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7292 (tp40) REVERT: A 76 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8595 (mm) REVERT: A 235 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7199 (m-10) outliers start: 21 outliers final: 13 residues processed: 82 average time/residue: 0.1342 time to fit residues: 13.5843 Evaluate side-chains 84 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7800 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3073 Z= 0.199 Angle : 0.658 7.770 4167 Z= 0.331 Chirality : 0.041 0.158 479 Planarity : 0.004 0.032 506 Dihedral : 4.308 19.368 405 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.33 % Allowed : 30.09 % Favored : 64.58 % 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: 2.02 (0.48), residues: 379 helix: 2.08 (0.30), residues: 315 sheet: -2.90 (1.34), residues: 10 loop : -2.39 (1.07), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.053 0.002 PHE A 262 TYR 0.013 0.001 TYR A 278 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.296 Fit side-chains REVERT: A 51 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7293 (tp40) REVERT: A 235 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.7148 (m-10) outliers start: 17 outliers final: 15 residues processed: 77 average time/residue: 0.1270 time to fit residues: 12.2149 Evaluate side-chains 83 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7847 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 : 0.004 0.043 3073 Z= 0.238 Angle : 0.685 8.920 4167 Z= 0.346 Chirality : 0.042 0.161 479 Planarity : 0.004 0.031 506 Dihedral : 4.415 17.573 405 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.96 % Allowed : 30.09 % Favored : 63.95 % 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: 1.88 (0.47), residues: 379 helix: 1.97 (0.30), residues: 315 sheet: -2.96 (1.34), residues: 10 loop : -2.39 (1.05), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.006 0.001 HIS A 379 PHE 0.012 0.002 PHE A 16 TYR 0.011 0.001 TYR A 278 ARG 0.001 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.325 Fit side-chains REVERT: A 51 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7285 (tp40) REVERT: A 76 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8544 (mm) REVERT: A 149 PHE cc_start: 0.6975 (t80) cc_final: 0.6658 (m-80) REVERT: A 235 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7319 (m-10) outliers start: 19 outliers final: 15 residues processed: 77 average time/residue: 0.1394 time to fit residues: 13.2328 Evaluate side-chains 80 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7825 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3073 Z= 0.218 Angle : 0.692 9.521 4167 Z= 0.347 Chirality : 0.041 0.158 479 Planarity : 0.004 0.032 506 Dihedral : 4.408 18.191 405 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.96 % Allowed : 31.03 % Favored : 63.01 % 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: 1.84 (0.47), residues: 379 helix: 1.92 (0.30), residues: 316 sheet: -2.92 (1.36), residues: 10 loop : -2.29 (1.06), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.011 0.001 PHE A 16 TYR 0.012 0.001 TYR A 278 ARG 0.001 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.332 Fit side-chains REVERT: A 51 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7318 (tp40) REVERT: A 76 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8566 (mm) REVERT: A 149 PHE cc_start: 0.6968 (t80) cc_final: 0.6509 (m-80) REVERT: A 235 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7388 (m-10) outliers start: 19 outliers final: 14 residues processed: 78 average time/residue: 0.1336 time to fit residues: 12.7524 Evaluate side-chains 82 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3073 Z= 0.239 Angle : 0.713 9.808 4167 Z= 0.360 Chirality : 0.043 0.160 479 Planarity : 0.004 0.032 506 Dihedral : 4.466 18.780 405 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.96 % Allowed : 29.78 % Favored : 64.26 % 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: 1.76 (0.47), residues: 379 helix: 1.89 (0.30), residues: 315 sheet: -2.82 (1.37), residues: 10 loop : -2.40 (1.06), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.014 0.002 PHE A 159 TYR 0.011 0.001 TYR A 278 ARG 0.001 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.326 Fit side-chains REVERT: A 51 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7266 (tp40) REVERT: A 76 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8555 (mm) REVERT: A 149 PHE cc_start: 0.6824 (t80) cc_final: 0.6357 (m-80) REVERT: A 235 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7429 (m-10) outliers start: 19 outliers final: 15 residues processed: 78 average time/residue: 0.1369 time to fit residues: 13.1745 Evaluate side-chains 84 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3073 Z= 0.219 Angle : 0.711 10.725 4167 Z= 0.357 Chirality : 0.042 0.162 479 Planarity : 0.004 0.033 506 Dihedral : 4.439 19.262 405 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.33 % Allowed : 31.03 % Favored : 63.64 % 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: 1.82 (0.47), residues: 379 helix: 1.91 (0.30), residues: 316 sheet: -2.81 (1.37), residues: 10 loop : -2.32 (1.06), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.013 0.001 PHE A 159 TYR 0.012 0.001 TYR A 278 ARG 0.001 0.000 ARG A 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.334 Fit side-chains REVERT: A 51 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7300 (tp40) REVERT: A 76 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 149 PHE cc_start: 0.6817 (t80) cc_final: 0.6337 (m-80) REVERT: A 235 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7365 (m-10) outliers start: 17 outliers final: 14 residues processed: 75 average time/residue: 0.1333 time to fit residues: 12.2665 Evaluate side-chains 82 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 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 = 0.3961 r_free = 0.3961 target = 0.169129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148915 restraints weight = 3850.076| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.92 r_work: 0.3648 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3073 Z= 0.242 Angle : 0.717 10.184 4167 Z= 0.361 Chirality : 0.043 0.160 479 Planarity : 0.004 0.032 506 Dihedral : 4.476 19.121 405 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.64 % Allowed : 30.72 % Favored : 63.64 % 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: 1.68 (0.47), residues: 379 helix: 1.91 (0.30), residues: 310 sheet: -2.79 (1.39), residues: 10 loop : -2.61 (0.97), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.006 0.001 HIS A 379 PHE 0.013 0.002 PHE A 159 TYR 0.011 0.001 TYR A 278 ARG 0.001 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1031.64 seconds wall clock time: 22 minutes 12.93 seconds (1332.93 seconds total)