Starting phenix.real_space_refine on Sun Mar 10 17:57:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/03_2024/7v0m_26944.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/03_2024/7v0m_26944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/03_2024/7v0m_26944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/03_2024/7v0m_26944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/03_2024/7v0m_26944.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/03_2024/7v0m_26944.pdb" } resolution = 2.7 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= 0.000 sd= 0.224 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2286 2.51 5 N 677 2.21 5 O 746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ASP 332": "OD1" <-> "OD2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W GLU 22": "OE1" <-> "OE2" 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: 3724 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3431 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 432} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 233 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 29} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.50, per 1000 atoms: 0.67 Number of scatterers: 3724 At special positions: 0 Unit cell: (95.45, 106.655, 58.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 746 8.00 N 677 7.00 C 2286 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: 1.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 64.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.508A pdb=" N ILE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 274 through 282 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'W' and resid 4 through 7 Processing helix chain 'W' and resid 8 through 17 removed outlier: 3.573A pdb=" N GLU W 17 " --> pdb=" O GLU W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 22 removed outlier: 3.537A pdb=" N GLU W 22 " --> pdb=" O GLU W 19 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 1.54 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: 1285 1.34 - 1.46: 646 1.46 - 1.58: 1770 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 3726 Sorted by residual: bond pdb=" CB LYS A 270 " pdb=" CG LYS A 270 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.93e-01 bond pdb=" CG LYS A 270 " pdb=" CD LYS A 270 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.12e-01 bond pdb=" CG1 ILE A 38 " pdb=" CD1 ILE A 38 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.55e-01 bond pdb=" CB ASN A 434 " pdb=" CG ASN A 434 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.02e-01 bond pdb=" CB VAL A 410 " pdb=" CG1 VAL A 410 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.92e-01 ... (remaining 3721 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.32: 108 106.32 - 112.58: 2006 112.58 - 118.84: 1054 118.84 - 125.10: 1843 125.10 - 131.36: 50 Bond angle restraints: 5061 Sorted by residual: angle pdb=" CB LYS A 270 " pdb=" CG LYS A 270 " pdb=" CD LYS A 270 " ideal model delta sigma weight residual 111.30 118.12 -6.82 2.30e+00 1.89e-01 8.78e+00 angle pdb=" N THR A 393 " pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 112.97 110.30 2.67 1.06e+00 8.90e-01 6.33e+00 angle pdb=" CB MET W 11 " pdb=" CG MET W 11 " pdb=" SD MET W 11 " ideal model delta sigma weight residual 112.70 120.21 -7.51 3.00e+00 1.11e-01 6.26e+00 angle pdb=" C ASP A 271 " pdb=" N GLU A 272 " pdb=" CA GLU A 272 " ideal model delta sigma weight residual 122.19 125.56 -3.37 1.41e+00 5.03e-01 5.70e+00 angle pdb=" C LYS A 436 " pdb=" N VAL A 437 " pdb=" CA VAL A 437 " ideal model delta sigma weight residual 121.97 117.97 4.00 1.80e+00 3.09e-01 4.93e+00 ... (remaining 5056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 1945 17.73 - 35.47: 234 35.47 - 53.20: 62 53.20 - 70.93: 19 70.93 - 88.67: 9 Dihedral angle restraints: 2269 sinusoidal: 876 harmonic: 1393 Sorted by residual: dihedral pdb=" CA VAL A 435 " pdb=" C VAL A 435 " pdb=" N LYS A 436 " pdb=" CA LYS A 436 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB GLU A 125 " pdb=" CG GLU A 125 " pdb=" CD GLU A 125 " pdb=" OE1 GLU A 125 " ideal model delta sinusoidal sigma weight residual 0.00 88.67 -88.67 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU W 17 " pdb=" CG GLU W 17 " pdb=" CD GLU W 17 " pdb=" OE1 GLU W 17 " ideal model delta sinusoidal sigma weight residual 0.00 86.56 -86.56 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 2266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 289 0.026 - 0.052: 180 0.052 - 0.078: 91 0.078 - 0.103: 34 0.103 - 0.129: 3 Chirality restraints: 597 Sorted by residual: chirality pdb=" CA ILE W 26 " pdb=" N ILE W 26 " pdb=" C ILE W 26 " pdb=" CB ILE W 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CG LEU A 424 " pdb=" CB LEU A 424 " pdb=" CD1 LEU A 424 " pdb=" CD2 LEU A 424 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA PRO A 308 " pdb=" N PRO A 308 " pdb=" C PRO A 308 " pdb=" CB PRO A 308 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.71e-01 ... (remaining 594 not shown) Planarity restraints: 668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 439 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 440 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 307 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO A 308 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 146 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 147 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 147 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 147 " -0.020 5.00e-02 4.00e+02 ... (remaining 665 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 675 2.77 - 3.30: 3676 3.30 - 3.84: 6821 3.84 - 4.37: 8248 4.37 - 4.90: 12869 Nonbonded interactions: 32289 Sorted by model distance: nonbonded pdb=" NH2 ARG A 182 " pdb=" OD1 ASP W 7 " model vdw 2.240 2.520 nonbonded pdb=" OH TYR A 166 " pdb=" O GLY A 170 " model vdw 2.257 2.440 nonbonded pdb=" O ASN A 103 " pdb=" O HOH A1901 " model vdw 2.284 2.440 nonbonded pdb=" O LEU A 71 " pdb=" O HOH A1902 " model vdw 2.298 2.440 nonbonded pdb=" O HOH A1918 " pdb=" O HOH A1939 " model vdw 2.322 2.440 ... (remaining 32284 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: 2.270 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: 6.460 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 0.036 3726 Z= 0.227 Angle : 0.563 7.505 5061 Z= 0.307 Chirality : 0.041 0.129 597 Planarity : 0.005 0.045 668 Dihedral : 18.103 88.666 1365 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.29 % Allowed : 20.16 % Favored : 78.55 % 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: 0.52 (0.36), residues: 479 helix: 0.73 (0.27), residues: 322 sheet: None (None), residues: 0 loop : -0.26 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 211 PHE 0.011 0.001 PHE A 234 TYR 0.013 0.002 TYR A 455 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.439 Fit side-chains REVERT: A 458 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6872 (mt0) outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 1.2262 time to fit residues: 88.5731 Evaluate side-chains 65 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 458 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS W 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3726 Z= 0.143 Angle : 0.423 4.993 5061 Z= 0.220 Chirality : 0.037 0.124 597 Planarity : 0.004 0.036 668 Dihedral : 5.529 70.904 514 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.10 % Allowed : 17.05 % Favored : 79.84 % 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: 1.44 (0.37), residues: 479 helix: 1.48 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.03 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 442 PHE 0.008 0.001 PHE A 234 TYR 0.006 0.001 TYR A 100 ARG 0.001 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.434 Fit side-chains REVERT: A 187 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7231 (mtp85) outliers start: 12 outliers final: 4 residues processed: 70 average time/residue: 1.2432 time to fit residues: 89.7476 Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.0040 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS W 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3726 Z= 0.120 Angle : 0.401 4.994 5061 Z= 0.207 Chirality : 0.036 0.122 597 Planarity : 0.004 0.032 668 Dihedral : 3.711 18.780 509 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.36 % Allowed : 17.05 % Favored : 79.59 % 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: 1.85 (0.38), residues: 479 helix: 1.81 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.06 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 244 PHE 0.007 0.001 PHE A 234 TYR 0.005 0.001 TYR A 216 ARG 0.001 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.486 Fit side-chains REVERT: A 66 HIS cc_start: 0.8273 (m170) cc_final: 0.7907 (m-70) REVERT: A 79 ASN cc_start: 0.8761 (m-40) cc_final: 0.8553 (m-40) REVERT: A 187 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7019 (mtp85) REVERT: A 454 LYS cc_start: 0.8523 (tttp) cc_final: 0.7569 (ttmp) outliers start: 13 outliers final: 4 residues processed: 72 average time/residue: 1.1175 time to fit residues: 83.2572 Evaluate side-chains 65 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3726 Z= 0.178 Angle : 0.442 5.090 5061 Z= 0.227 Chirality : 0.038 0.121 597 Planarity : 0.004 0.032 668 Dihedral : 3.924 19.477 509 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.13 % Allowed : 16.54 % Favored : 79.33 % 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: 1.80 (0.38), residues: 479 helix: 1.78 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.04 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 383 PHE 0.010 0.001 PHE A 234 TYR 0.008 0.001 TYR A 455 ARG 0.001 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.454 Fit side-chains REVERT: A 187 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7289 (mtp85) REVERT: A 454 LYS cc_start: 0.8423 (tttp) cc_final: 0.7764 (ttmp) REVERT: A 458 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6868 (mp10) outliers start: 16 outliers final: 6 residues processed: 70 average time/residue: 1.1825 time to fit residues: 85.5460 Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 458 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.0570 chunk 27 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 183 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3726 Z= 0.124 Angle : 0.408 5.093 5061 Z= 0.209 Chirality : 0.036 0.120 597 Planarity : 0.004 0.032 668 Dihedral : 3.689 18.254 509 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.36 % Allowed : 17.83 % Favored : 78.81 % 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: 1.99 (0.38), residues: 479 helix: 1.94 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.07 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.007 0.001 PHE A 234 TYR 0.006 0.001 TYR A 455 ARG 0.001 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.452 Fit side-chains REVERT: A 66 HIS cc_start: 0.8319 (m170) cc_final: 0.7985 (m-70) REVERT: A 187 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6994 (mtp85) REVERT: A 454 LYS cc_start: 0.8361 (tttp) cc_final: 0.7721 (ttmp) outliers start: 13 outliers final: 6 residues processed: 71 average time/residue: 1.3590 time to fit residues: 99.4170 Evaluate side-chains 70 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain W residue 31 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3726 Z= 0.249 Angle : 0.489 5.187 5061 Z= 0.252 Chirality : 0.041 0.119 597 Planarity : 0.004 0.031 668 Dihedral : 4.113 20.102 509 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.65 % Allowed : 17.31 % Favored : 78.04 % 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: 1.75 (0.37), residues: 479 helix: 1.74 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.01 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 162 PHE 0.013 0.001 PHE A 234 TYR 0.007 0.002 TYR A 455 ARG 0.003 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.409 Fit side-chains REVERT: A 187 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6986 (mtp85) REVERT: A 454 LYS cc_start: 0.8467 (tttp) cc_final: 0.8217 (tttp) REVERT: A 458 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6735 (mp10) outliers start: 18 outliers final: 10 residues processed: 74 average time/residue: 1.1972 time to fit residues: 91.5609 Evaluate side-chains 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain W residue 31 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3726 Z= 0.155 Angle : 0.436 5.119 5061 Z= 0.224 Chirality : 0.038 0.119 597 Planarity : 0.004 0.033 668 Dihedral : 3.888 19.406 509 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.65 % Allowed : 17.05 % Favored : 78.29 % 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 (0.38), residues: 479 helix: 1.86 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.01 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.009 0.001 PHE A 234 TYR 0.005 0.001 TYR A 100 ARG 0.003 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.376 Fit side-chains REVERT: A 187 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7317 (mtp85) REVERT: A 454 LYS cc_start: 0.8417 (tttp) cc_final: 0.8157 (tttp) REVERT: A 458 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6705 (mp10) outliers start: 18 outliers final: 10 residues processed: 74 average time/residue: 1.2445 time to fit residues: 94.9700 Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain W residue 31 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.0770 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3726 Z= 0.118 Angle : 0.411 5.492 5061 Z= 0.210 Chirality : 0.036 0.117 597 Planarity : 0.004 0.033 668 Dihedral : 3.610 17.457 509 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.10 % Allowed : 18.86 % Favored : 78.04 % 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: 2.07 (0.38), residues: 479 helix: 2.01 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.09 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 83 PHE 0.005 0.001 PHE A 234 TYR 0.005 0.001 TYR A 216 ARG 0.004 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.467 Fit side-chains REVERT: A 79 ASN cc_start: 0.8774 (m-40) cc_final: 0.8534 (m-40) REVERT: A 187 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7245 (mtp85) REVERT: A 401 THR cc_start: 0.8346 (p) cc_final: 0.8103 (p) REVERT: A 454 LYS cc_start: 0.8380 (tttp) cc_final: 0.7711 (ttmp) REVERT: A 458 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6578 (mp10) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 1.1964 time to fit residues: 91.5249 Evaluate side-chains 77 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain W residue 31 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3726 Z= 0.250 Angle : 0.501 6.484 5061 Z= 0.257 Chirality : 0.041 0.118 597 Planarity : 0.004 0.031 668 Dihedral : 4.087 19.986 509 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.88 % Allowed : 18.60 % Favored : 77.52 % 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 (0.38), residues: 479 helix: 1.77 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.01 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.013 0.001 PHE A 234 TYR 0.007 0.002 TYR A 455 ARG 0.004 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.452 Fit side-chains REVERT: A 187 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7360 (mtp85) REVERT: A 454 LYS cc_start: 0.8459 (tttp) cc_final: 0.7876 (ttmp) REVERT: A 458 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6863 (mp10) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 1.2330 time to fit residues: 90.3064 Evaluate side-chains 74 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain W residue 31 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3726 Z= 0.197 Angle : 0.475 6.789 5061 Z= 0.243 Chirality : 0.039 0.118 597 Planarity : 0.004 0.032 668 Dihedral : 4.018 19.877 509 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.36 % Allowed : 19.38 % Favored : 77.26 % 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: 1.75 (0.37), residues: 479 helix: 1.77 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.05 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.011 0.001 PHE A 234 TYR 0.006 0.001 TYR A 100 ARG 0.004 0.000 ARG A 426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.441 Fit side-chains REVERT: A 187 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7346 (mtp85) REVERT: A 454 LYS cc_start: 0.8439 (tttp) cc_final: 0.7781 (ttmp) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 1.1835 time to fit residues: 85.6233 Evaluate side-chains 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain W residue 31 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.126093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.106548 restraints weight = 4025.997| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.39 r_work: 0.2892 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3726 Z= 0.146 Angle : 0.445 6.943 5061 Z= 0.228 Chirality : 0.037 0.117 597 Planarity : 0.004 0.032 668 Dihedral : 3.824 18.979 509 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.84 % Allowed : 19.90 % Favored : 77.26 % 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: 1.88 (0.38), residues: 479 helix: 1.87 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.00 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.008 0.001 PHE A 234 TYR 0.012 0.001 TYR A 455 ARG 0.004 0.000 ARG A 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2474.08 seconds wall clock time: 44 minutes 14.00 seconds (2654.00 seconds total)