Starting phenix.real_space_refine (version: dev) on Fri Feb 17 06:45:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/02_2023/7v0m_26944.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/02_2023/7v0m_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_26944/02_2023/7v0m_26944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/02_2023/7v0m_26944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/02_2023/7v0m_26944.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0m_26944/02_2023/7v0m_26944.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 2.32, per 1000 atoms: 0.62 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: 1.26 Conformation dependent library (CDL) restraints added in 604.4 milliseconds 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: 0.17 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: 0.85 Time building geometry restraints manager: 1.40 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 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. 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.470 Check model and map are aligned: 0.060 Process input model: 12.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 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 % 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 *********************** 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 : 0.487 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 1.2909 time to fit residues: 93.2202 Evaluate side-chains 64 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8820 moved from start: 0.0690 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= 0.147 Angle : 0.430 5.042 5061 Z= 0.224 Chirality : 0.037 0.124 597 Planarity : 0.004 0.035 668 Dihedral : 4.013 19.939 509 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 3.88 % 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: 1.40 (0.37), residues: 479 helix: 1.45 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.05 (0.49), residues: 155 *********************** 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 77 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.486 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 71 average time/residue: 1.2870 time to fit residues: 94.2318 Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1419 time to fit residues: 0.9351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.8853 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3726 Z= 0.220 Angle : 0.476 5.115 5061 Z= 0.247 Chirality : 0.040 0.124 597 Planarity : 0.004 0.032 668 Dihedral : 4.154 20.866 509 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 4.13 % 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: 1.50 (0.37), residues: 479 helix: 1.54 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.04 (0.49), residues: 155 *********************** 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 79 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.476 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 74 average time/residue: 1.1498 time to fit residues: 88.1176 Evaluate side-chains 66 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1357 time to fit residues: 0.9500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 0.0040 chunk 43 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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: 0.8800 moved from start: 0.0998 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 : 0.405 5.010 5061 Z= 0.208 Chirality : 0.036 0.122 597 Planarity : 0.004 0.032 668 Dihedral : 3.752 19.025 509 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 3.62 % 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 : 0.02 (0.50), residues: 155 *********************** 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: 14 poor density : 64 time to evaluate : 0.405 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 73 average time/residue: 1.1378 time to fit residues: 86.1096 Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.433 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1387 time to fit residues: 0.9174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 79 ASN A 183 ASN W 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 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 : 0.003 0.030 3726 Z= 0.174 Angle : 0.441 5.108 5061 Z= 0.226 Chirality : 0.038 0.120 597 Planarity : 0.004 0.032 668 Dihedral : 3.906 19.548 509 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.38), residues: 479 helix: 1.85 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.02 (0.50), residues: 155 *********************** 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 76 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.412 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 1.0840 time to fit residues: 79.7258 Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1261 time to fit residues: 0.8886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 79 ASN A 183 ASN A 237 GLN W 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 3726 Z= 0.280 Angle : 0.509 5.206 5061 Z= 0.263 Chirality : 0.042 0.120 597 Planarity : 0.004 0.032 668 Dihedral : 4.240 20.976 509 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 5.43 % 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: 1.67 (0.37), residues: 479 helix: 1.70 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.07 (0.49), residues: 155 *********************** 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: 21 poor density : 60 time to evaluate : 0.450 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 75 average time/residue: 1.0849 time to fit residues: 84.3713 Evaluate side-chains 67 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1457 time to fit residues: 0.9858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.0070 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 79 ASN A 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 3726 Z= 0.120 Angle : 0.413 5.217 5061 Z= 0.212 Chirality : 0.036 0.119 597 Planarity : 0.004 0.034 668 Dihedral : 3.767 18.957 509 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 3.62 % 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: 1.98 (0.38), residues: 479 helix: 1.94 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.04 (0.50), residues: 155 *********************** 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 76 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.441 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 1.1917 time to fit residues: 87.5773 Evaluate side-chains 70 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1742 time to fit residues: 0.7495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 0.0060 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 237 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 3726 Z= 0.148 Angle : 0.446 6.537 5061 Z= 0.227 Chirality : 0.037 0.118 597 Planarity : 0.004 0.033 668 Dihedral : 3.794 18.652 509 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 3.88 % 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: 1.93 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.09 (0.50), residues: 155 *********************** 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 79 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.490 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 1.1945 time to fit residues: 92.6894 Evaluate side-chains 70 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.2629 time to fit residues: 0.9568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 3726 Z= 0.248 Angle : 0.501 6.528 5061 Z= 0.257 Chirality : 0.041 0.118 597 Planarity : 0.004 0.031 668 Dihedral : 4.128 20.271 509 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 3.62 % 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: 1.79 (0.38), residues: 479 helix: 1.77 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.02 (0.50), residues: 155 *********************** 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 75 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.457 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 71 average time/residue: 1.1808 time to fit residues: 86.6751 Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1324 time to fit residues: 0.8896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 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 0.027 3726 Z= 0.152 Angle : 0.452 6.876 5061 Z= 0.232 Chirality : 0.038 0.120 597 Planarity : 0.004 0.033 668 Dihedral : 3.897 19.015 509 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.38), residues: 479 helix: 1.86 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.06 (0.50), residues: 155 ********************** 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 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.470 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 1.3239 time to fit residues: 95.8065 Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.6105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 0.0980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.125519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.106038 restraints weight = 4011.459| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.38 r_work: 0.2873 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3726 Z= 0.183 Angle : 0.470 6.858 5061 Z= 0.241 Chirality : 0.039 0.117 597 Planarity : 0.004 0.032 668 Dihedral : 3.964 19.302 509 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.38), residues: 479 helix: 1.80 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.05 (0.50), residues: 155 =============================================================================== Job complete usr+sys time: 2328.41 seconds wall clock time: 42 minutes 8.94 seconds (2528.94 seconds total)