Starting phenix.real_space_refine on Sun Mar 10 14:50:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5c_36901/03_2024/8k5c_36901_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5c_36901/03_2024/8k5c_36901.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5c_36901/03_2024/8k5c_36901_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5c_36901/03_2024/8k5c_36901_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5c_36901/03_2024/8k5c_36901_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5c_36901/03_2024/8k5c_36901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5c_36901/03_2024/8k5c_36901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5c_36901/03_2024/8k5c_36901_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5c_36901/03_2024/8k5c_36901_updated.pdb" } resolution = 3.13 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= -0.002 sd= 0.041 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 21 5.16 5 C 1588 2.51 5 N 397 2.21 5 O 374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2380 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2369 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'OJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.80 Number of scatterers: 2380 At special positions: 0 Unit cell: (61.005, 70.965, 73.455, 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 21 16.00 O 374 8.00 N 397 7.00 C 1588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " 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 487.5 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: 9 helices and 0 sheets defined 71.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 30 through 53 Processing helix chain 'A' and resid 62 through 89 Proline residue: A 81 - end of helix removed outlier: 3.904A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 129 Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 141 through 162 removed outlier: 5.048A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 6.026A 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 260 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.531A pdb=" N ARG A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER A 271 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A 280 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 290 " --> pdb=" O SER A 287 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.855A pdb=" N TYR A 294 " --> pdb=" O PRO A 291 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 411 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: 0.59 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 344 1.32 - 1.45: 730 1.45 - 1.57: 1343 1.57 - 1.70: 0 1.70 - 1.83: 31 Bond restraints: 2448 Sorted by residual: bond pdb=" C PRO A 99 " pdb=" O PRO A 99 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.16e-02 7.43e+03 1.55e+01 bond pdb=" C ILE A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.336 1.359 -0.024 1.23e-02 6.61e+03 3.73e+00 bond pdb=" SD MET A 103 " pdb=" CE MET A 103 " ideal model delta sigma weight residual 1.791 1.754 0.037 2.50e-02 1.60e+03 2.24e+00 bond pdb=" CA PRO A 99 " pdb=" C PRO A 99 " ideal model delta sigma weight residual 1.517 1.536 -0.019 1.54e-02 4.22e+03 1.59e+00 bond pdb=" C MET A 167 " pdb=" N PRO A 168 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.24e+00 ... (remaining 2443 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.52: 56 106.52 - 113.42: 1337 113.42 - 120.32: 935 120.32 - 127.22: 958 127.22 - 134.13: 35 Bond angle restraints: 3321 Sorted by residual: angle pdb=" C PRO A 99 " pdb=" CA PRO A 99 " pdb=" CB PRO A 99 " ideal model delta sigma weight residual 112.11 116.62 -4.51 1.46e+00 4.69e-01 9.53e+00 angle pdb=" CA MET A 103 " pdb=" CB MET A 103 " pdb=" CG MET A 103 " ideal model delta sigma weight residual 114.10 108.41 5.69 2.00e+00 2.50e-01 8.10e+00 angle pdb=" N PRO A 99 " pdb=" CA PRO A 99 " pdb=" C PRO A 99 " ideal model delta sigma weight residual 113.57 109.93 3.64 1.31e+00 5.83e-01 7.73e+00 angle pdb=" CA PRO A 99 " pdb=" C PRO A 99 " pdb=" O PRO A 99 " ideal model delta sigma weight residual 119.34 115.72 3.62 1.47e+00 4.63e-01 6.06e+00 angle pdb=" CA MET A 167 " pdb=" CB MET A 167 " pdb=" CG MET A 167 " ideal model delta sigma weight residual 114.10 118.61 -4.51 2.00e+00 2.50e-01 5.08e+00 ... (remaining 3316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 1157 15.13 - 30.26: 177 30.26 - 45.39: 70 45.39 - 60.52: 15 60.52 - 75.65: 2 Dihedral angle restraints: 1421 sinusoidal: 567 harmonic: 854 Sorted by residual: dihedral pdb=" CA MET A 167 " pdb=" C MET A 167 " pdb=" N PRO A 168 " pdb=" CA PRO A 168 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE A 197 " pdb=" C PHE A 197 " pdb=" N PHE A 198 " pdb=" CA PHE A 198 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB CYS A 19 " pdb=" SG CYS A 19 " pdb=" SG CYS A 266 " pdb=" CB CYS A 266 " ideal model delta sinusoidal sigma weight residual -86.00 -54.87 -31.13 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 1418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 213 0.028 - 0.056: 107 0.056 - 0.084: 37 0.084 - 0.111: 18 0.111 - 0.139: 4 Chirality restraints: 379 Sorted by residual: chirality pdb=" CA LEU A 30 " pdb=" N LEU A 30 " pdb=" C LEU A 30 " pdb=" CB LEU A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CB THR A 279 " pdb=" CA THR A 279 " pdb=" OG1 THR A 279 " pdb=" CG2 THR A 279 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA PRO A 200 " pdb=" N PRO A 200 " pdb=" C PRO A 200 " pdb=" CB PRO A 200 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 376 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 31 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 245 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO A 246 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 98 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C ILE A 98 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 98 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 99 " 0.010 2.00e-02 2.50e+03 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 828 2.85 - 3.36: 2342 3.36 - 3.88: 3935 3.88 - 4.39: 4398 4.39 - 4.90: 7703 Nonbonded interactions: 19206 Sorted by model distance: nonbonded pdb=" OG SER A 62 " pdb=" OD2 ASP A 124 " model vdw 2.341 2.440 nonbonded pdb=" O GLY A 41 " pdb=" ND2 ASN A 45 " model vdw 2.365 2.520 nonbonded pdb=" O HIS A 131 " pdb=" ND2 ASN A 137 " model vdw 2.416 2.520 nonbonded pdb=" OG SER A 179 " pdb=" NE2 HIS A 189 " model vdw 2.416 2.520 nonbonded pdb=" OH TYR A 284 " pdb=" N05 OJX A 401 " model vdw 2.486 3.120 ... (remaining 19201 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: 0.480 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: 1.930 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.580 Find NCS groups from input model: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2448 Z= 0.224 Angle : 0.633 7.587 3321 Z= 0.344 Chirality : 0.041 0.139 379 Planarity : 0.006 0.048 402 Dihedral : 17.071 75.648 854 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.78 % Allowed : 25.97 % Favored : 73.26 % 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: 0.59 (0.50), residues: 289 helix: 1.44 (0.36), residues: 198 sheet: None (None), residues: 0 loop : -2.05 (0.64), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 256 HIS 0.002 0.001 HIS A 55 PHE 0.009 0.001 PHE A 82 TYR 0.003 0.001 TYR A 126 ARG 0.002 0.000 ARG A 101 *********************** 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 33 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.279 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.2473 time to fit residues: 8.9472 Evaluate side-chains 32 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7566 moved from start: 0.0488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2448 Z= 0.220 Angle : 0.565 6.884 3321 Z= 0.305 Chirality : 0.040 0.130 379 Planarity : 0.006 0.050 402 Dihedral : 5.874 57.276 316 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.10 % Allowed : 23.64 % Favored : 73.26 % 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: 0.54 (0.48), residues: 289 helix: 1.44 (0.35), residues: 199 sheet: None (None), residues: 0 loop : -2.18 (0.63), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 256 HIS 0.002 0.001 HIS A 55 PHE 0.017 0.001 PHE A 232 TYR 0.004 0.001 TYR A 269 ARG 0.002 0.000 ARG A 89 *********************** 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 38 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.252 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 35 average time/residue: 0.2238 time to fit residues: 9.0388 Evaluate side-chains 34 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2448 Z= 0.258 Angle : 0.593 6.811 3321 Z= 0.313 Chirality : 0.041 0.132 379 Planarity : 0.006 0.050 402 Dihedral : 5.343 54.304 314 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.26 % Allowed : 23.64 % Favored : 72.09 % 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: 0.40 (0.48), residues: 289 helix: 1.34 (0.34), residues: 199 sheet: None (None), residues: 0 loop : -2.28 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 256 HIS 0.003 0.001 HIS A 189 PHE 0.016 0.002 PHE A 232 TYR 0.005 0.001 TYR A 126 ARG 0.002 0.000 ARG A 89 *********************** 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 40 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.277 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 36 average time/residue: 0.2104 time to fit residues: 8.7586 Evaluate side-chains 35 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 259 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.7608 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2448 Z= 0.267 Angle : 0.584 6.690 3321 Z= 0.311 Chirality : 0.041 0.137 379 Planarity : 0.006 0.051 402 Dihedral : 5.259 50.808 314 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.65 % Allowed : 22.87 % Favored : 72.48 % 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: 0.26 (0.48), residues: 289 helix: 1.23 (0.34), residues: 199 sheet: None (None), residues: 0 loop : -2.31 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 256 HIS 0.003 0.001 HIS A 189 PHE 0.015 0.002 PHE A 232 TYR 0.005 0.001 TYR A 126 ARG 0.003 0.000 ARG A 89 *********************** 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 40 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 28 time to evaluate : 0.247 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 36 average time/residue: 0.1846 time to fit residues: 7.7392 Evaluate side-chains 34 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7612 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2448 Z= 0.273 Angle : 0.601 6.718 3321 Z= 0.319 Chirality : 0.042 0.134 379 Planarity : 0.006 0.052 402 Dihedral : 5.256 49.287 314 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.04 % Allowed : 24.03 % Favored : 70.93 % 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: 0.23 (0.48), residues: 289 helix: 1.20 (0.34), residues: 199 sheet: None (None), residues: 0 loop : -2.31 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 256 HIS 0.002 0.001 HIS A 189 PHE 0.015 0.002 PHE A 232 TYR 0.005 0.001 TYR A 126 ARG 0.002 0.000 ARG A 89 *********************** 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 40 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 27 time to evaluate : 0.197 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 36 average time/residue: 0.1455 time to fit residues: 6.1330 Evaluate side-chains 36 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 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: 0.7596 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2448 Z= 0.223 Angle : 0.560 6.734 3321 Z= 0.300 Chirality : 0.040 0.135 379 Planarity : 0.006 0.052 402 Dihedral : 5.028 44.761 314 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.65 % Allowed : 22.87 % Favored : 72.48 % 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: 0.38 (0.48), residues: 289 helix: 1.32 (0.34), residues: 199 sheet: None (None), residues: 0 loop : -2.27 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 256 HIS 0.003 0.001 HIS A 55 PHE 0.014 0.001 PHE A 232 TYR 0.004 0.001 TYR A 126 ARG 0.002 0.000 ARG A 89 *********************** 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 41 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 29 time to evaluate : 0.282 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 37 average time/residue: 0.1831 time to fit residues: 7.9742 Evaluate side-chains 36 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.0010 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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: 0.7582 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2448 Z= 0.214 Angle : 0.555 6.645 3321 Z= 0.300 Chirality : 0.040 0.130 379 Planarity : 0.006 0.051 402 Dihedral : 4.946 42.395 314 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.88 % Allowed : 24.03 % Favored : 72.09 % 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: 0.45 (0.49), residues: 289 helix: 1.37 (0.34), residues: 199 sheet: None (None), residues: 0 loop : -2.24 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 256 HIS 0.001 0.000 HIS A 55 PHE 0.013 0.001 PHE A 232 TYR 0.004 0.001 TYR A 126 ARG 0.002 0.000 ARG A 89 *********************** 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 38 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.248 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 36 average time/residue: 0.1820 time to fit residues: 7.7296 Evaluate side-chains 35 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7596 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2448 Z= 0.248 Angle : 0.577 6.624 3321 Z= 0.310 Chirality : 0.041 0.133 379 Planarity : 0.006 0.052 402 Dihedral : 5.029 43.342 314 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.26 % Allowed : 23.26 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.49), residues: 289 helix: 1.35 (0.34), residues: 199 sheet: None (None), residues: 0 loop : -2.24 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 256 HIS 0.002 0.001 HIS A 55 PHE 0.014 0.001 PHE A 232 TYR 0.005 0.001 TYR A 126 ARG 0.002 0.000 ARG A 89 *********************** 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 40 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.246 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 37 average time/residue: 0.2050 time to fit residues: 8.8976 Evaluate side-chains 37 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 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: 0.7588 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2448 Z= 0.234 Angle : 0.574 6.626 3321 Z= 0.309 Chirality : 0.041 0.162 379 Planarity : 0.006 0.052 402 Dihedral : 4.985 42.004 314 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.88 % Allowed : 23.64 % Favored : 72.48 % 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: 0.47 (0.49), residues: 289 helix: 1.25 (0.34), residues: 206 sheet: None (None), residues: 0 loop : -2.12 (0.69), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 256 HIS 0.001 0.000 HIS A 55 PHE 0.013 0.001 PHE A 232 TYR 0.004 0.001 TYR A 126 ARG 0.002 0.000 ARG A 89 *********************** 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 38 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.267 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 35 average time/residue: 0.1934 time to fit residues: 7.9005 Evaluate side-chains 37 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7582 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2448 Z= 0.230 Angle : 0.568 6.661 3321 Z= 0.306 Chirality : 0.041 0.133 379 Planarity : 0.006 0.052 402 Dihedral : 4.939 40.589 314 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.49 % Allowed : 24.03 % Favored : 72.48 % 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: 0.54 (0.49), residues: 289 helix: 1.30 (0.34), residues: 206 sheet: None (None), residues: 0 loop : -2.10 (0.69), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 256 HIS 0.002 0.001 HIS A 55 PHE 0.013 0.001 PHE A 232 TYR 0.004 0.001 TYR A 126 ARG 0.002 0.000 ARG A 89 ********************** 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 37 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.281 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 34 average time/residue: 0.1996 time to fit residues: 7.9371 Evaluate side-chains 37 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.153481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.138303 restraints weight = 2969.751| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.39 r_work: 0.3417 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2448 Z= 0.267 Angle : 0.588 6.694 3321 Z= 0.317 Chirality : 0.042 0.134 379 Planarity : 0.006 0.053 402 Dihedral : 5.080 42.725 314 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.26 % Allowed : 23.26 % Favored : 72.48 % 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 (0.49), residues: 289 helix: 1.30 (0.34), residues: 203 sheet: None (None), residues: 0 loop : -2.16 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 256 HIS 0.002 0.001 HIS A 189 PHE 0.014 0.002 PHE A 232 TYR 0.005 0.001 TYR A 126 ARG 0.002 0.000 ARG A 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 960.14 seconds wall clock time: 18 minutes 12.26 seconds (1092.26 seconds total)