Starting phenix.real_space_refine on Fri Dec 27 08:39:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0m_26944/12_2024/7v0m_26944.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0m_26944/12_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/cci-nas-00/data/ceres_data/7v0m_26944/12_2024/7v0m_26944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0m_26944/12_2024/7v0m_26944.map" model { file = "/net/cci-nas-00/data/ceres_data/7v0m_26944/12_2024/7v0m_26944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0m_26944/12_2024/7v0m_26944.cif" } 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. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.17, per 1000 atoms: 0.85 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 - 3.00 Amino acid : True - 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: 0.94 Conformation dependent library (CDL) restraints added in 477.3 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: 0.40 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: 0.99 Time building geometry restraints manager: 1.06 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: 0.00 - 1.50: 4935 1.50 - 3.00: 103 3.00 - 4.50: 19 4.50 - 6.00: 2 6.00 - 7.51: 2 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 3.120 nonbonded pdb=" OH TYR A 166 " pdb=" O GLY A 170 " model vdw 2.257 3.040 nonbonded pdb=" O ASN A 103 " pdb=" O HOH A1901 " model vdw 2.284 3.040 nonbonded pdb=" O LEU A 71 " pdb=" O HOH A1902 " model vdw 2.298 3.040 nonbonded pdb=" O HOH A1918 " pdb=" O HOH A1939 " model vdw 2.322 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.750 Find NCS groups from input model: 0.040 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.429 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: 1.2195 time to fit residues: 88.1064 Evaluate side-chains 65 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 0.6980 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8574 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3726 Z= 0.132 Angle : 0.421 5.013 5061 Z= 0.219 Chirality : 0.037 0.125 597 Planarity : 0.004 0.035 668 Dihedral : 5.370 72.880 514 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.84 % Allowed : 17.05 % Favored : 80.10 % 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: 1.48 (0.37), residues: 479 helix: 1.47 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.06 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 83 PHE 0.008 0.001 PHE A 234 TYR 0.006 0.001 TYR A 100 ARG 0.002 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 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.435 Fit side-chains REVERT: A 66 HIS cc_start: 0.8296 (m170) cc_final: 0.7935 (m-70) REVERT: A 187 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7019 (mtp85) outliers start: 11 outliers final: 2 residues processed: 68 average time/residue: 1.4047 time to fit residues: 98.4489 Evaluate side-chains 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 320 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN W 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3726 Z= 0.247 Angle : 0.488 5.145 5061 Z= 0.254 Chirality : 0.041 0.123 597 Planarity : 0.004 0.033 668 Dihedral : 4.218 20.901 509 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.62 % Allowed : 17.05 % 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: 1.49 (0.37), residues: 479 helix: 1.49 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.05 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 383 PHE 0.014 0.001 PHE A 234 TYR 0.007 0.002 TYR A 100 ARG 0.001 0.000 ARG A 286 *********************** 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 75 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.442 Fit side-chains REVERT: A 66 HIS cc_start: 0.8447 (m170) cc_final: 0.8015 (m-70) REVERT: A 187 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7024 (mtp85) REVERT: A 454 LYS cc_start: 0.8598 (tttp) cc_final: 0.8396 (tttp) outliers start: 14 outliers final: 5 residues processed: 70 average time/residue: 1.2583 time to fit residues: 91.0172 Evaluate side-chains 62 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 201 VAL 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: 0.3980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 38 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1030 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= 0.130 Angle : 0.417 5.311 5061 Z= 0.215 Chirality : 0.037 0.122 597 Planarity : 0.004 0.034 668 Dihedral : 3.812 18.901 509 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.36 % Allowed : 17.31 % 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: 1.84 (0.38), residues: 479 helix: 1.78 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.12 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 83 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 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 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.448 Fit side-chains REVERT: A 187 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7249 (mtp85) REVERT: A 454 LYS cc_start: 0.8533 (tttp) cc_final: 0.7477 (ttmp) outliers start: 13 outliers final: 5 residues processed: 66 average time/residue: 1.3211 time to fit residues: 90.0111 Evaluate side-chains 66 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 403 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.0060 chunk 27 optimal weight: 0.8980 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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: 0.8584 moved from start: 0.1097 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= 0.134 Angle : 0.421 5.088 5061 Z= 0.216 Chirality : 0.037 0.121 597 Planarity : 0.004 0.034 668 Dihedral : 3.745 18.333 509 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.10 % Allowed : 17.83 % Favored : 79.07 % 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: 1.92 (0.38), residues: 479 helix: 1.84 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.15 (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 0.007 0.001 TYR A 455 ARG 0.003 0.000 ARG A 426 *********************** 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 73 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.397 Fit side-chains REVERT: A 66 HIS cc_start: 0.8353 (m170) cc_final: 0.7972 (m-70) REVERT: A 187 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6985 (mtp85) REVERT: A 458 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6724 (mp10) outliers start: 12 outliers final: 5 residues processed: 66 average time/residue: 1.3246 time to fit residues: 90.2160 Evaluate side-chains 67 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 403 SER Chi-restraints excluded: chain A residue 458 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** 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: 0.8601 moved from start: 0.1036 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= 0.163 Angle : 0.444 5.888 5061 Z= 0.228 Chirality : 0.038 0.120 597 Planarity : 0.004 0.035 668 Dihedral : 3.850 18.610 509 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.88 % Allowed : 17.05 % Favored : 79.07 % 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: 1.89 (0.38), residues: 479 helix: 1.82 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.14 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 383 PHE 0.009 0.001 PHE A 234 TYR 0.006 0.001 TYR A 100 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 77 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.447 Fit side-chains REVERT: A 187 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7248 (mtp85) REVERT: A 454 LYS cc_start: 0.8498 (tttp) cc_final: 0.7649 (ttmp) REVERT: A 458 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6801 (mp10) outliers start: 15 outliers final: 5 residues processed: 69 average time/residue: 1.3047 time to fit residues: 92.8010 Evaluate side-chains 67 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 403 SER Chi-restraints excluded: chain A residue 458 GLN 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: 0.7980 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.8630 moved from start: 0.1021 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= 0.234 Angle : 0.494 6.045 5061 Z= 0.254 Chirality : 0.040 0.118 597 Planarity : 0.004 0.035 668 Dihedral : 4.108 20.092 509 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.39 % Allowed : 16.80 % 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: 1.78 (0.37), residues: 479 helix: 1.72 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.12 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 383 PHE 0.013 0.001 PHE A 234 TYR 0.007 0.002 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 81 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.423 Fit side-chains REVERT: A 187 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7284 (mtp85) REVERT: A 454 LYS cc_start: 0.8537 (tttp) cc_final: 0.7893 (ttmp) REVERT: A 458 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6808 (mp10) outliers start: 17 outliers final: 6 residues processed: 74 average time/residue: 1.2053 time to fit residues: 92.1426 Evaluate side-chains 68 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 201 VAL 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 458 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8592 moved from start: 0.1150 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= 0.144 Angle : 0.440 6.617 5061 Z= 0.225 Chirality : 0.037 0.119 597 Planarity : 0.004 0.035 668 Dihedral : 3.829 18.524 509 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.10 % Allowed : 18.60 % 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: 1.98 (0.38), residues: 479 helix: 1.86 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.23 (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 0.006 0.001 TYR A 100 ARG 0.003 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 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.469 Fit side-chains REVERT: A 187 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7236 (mtp85) REVERT: A 454 LYS cc_start: 0.8477 (tttp) cc_final: 0.7828 (ttmp) REVERT: A 458 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6792 (mp10) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 1.2912 time to fit residues: 90.6017 Evaluate side-chains 68 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 458 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 237 GLN ** 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: 0.8596 moved from start: 0.1144 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= 0.153 Angle : 0.449 6.709 5061 Z= 0.230 Chirality : 0.038 0.118 597 Planarity : 0.004 0.035 668 Dihedral : 3.836 18.517 509 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.36 % Allowed : 18.09 % 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: 1.98 (0.38), residues: 479 helix: 1.86 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.26 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 162 PHE 0.009 0.001 PHE A 234 TYR 0.006 0.001 TYR A 100 ARG 0.002 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 75 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.442 Fit side-chains REVERT: A 187 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7244 (mtp85) REVERT: A 454 LYS cc_start: 0.8478 (tttp) cc_final: 0.7861 (ttmp) REVERT: A 458 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6823 (mp10) outliers start: 13 outliers final: 7 residues processed: 72 average time/residue: 1.1958 time to fit residues: 89.0392 Evaluate side-chains 71 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 201 VAL 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 458 GLN Chi-restraints excluded: chain W residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1125 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= 0.186 Angle : 0.477 6.839 5061 Z= 0.244 Chirality : 0.039 0.118 597 Planarity : 0.004 0.035 668 Dihedral : 3.968 19.180 509 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: 1.90 (0.38), residues: 479 helix: 1.79 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.24 (0.50), 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 0.012 0.002 TYR A 455 ARG 0.001 0.000 ARG A 95 ********************** 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 to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.391 Fit side-chains REVERT: A 187 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7273 (mtp85) REVERT: A 454 LYS cc_start: 0.8491 (tttp) cc_final: 0.7880 (ttmp) REVERT: A 458 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6829 (mp10) outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 1.2487 time to fit residues: 90.5282 Evaluate side-chains 70 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 201 VAL 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 458 GLN Chi-restraints excluded: chain W residue 13 GLU 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: 3.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 32 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 237 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.129322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.110129 restraints weight = 4054.174| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.38 r_work: 0.2923 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1309 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= 0.126 Angle : 0.436 6.949 5061 Z= 0.222 Chirality : 0.036 0.119 597 Planarity : 0.004 0.035 668 Dihedral : 3.659 17.207 509 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.07 % Allowed : 20.16 % Favored : 77.78 % 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: 2.09 (0.38), residues: 479 helix: 1.93 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.34 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 83 PHE 0.006 0.001 PHE A 234 TYR 0.005 0.001 TYR A 100 ARG 0.002 0.000 ARG A 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.45 seconds wall clock time: 44 minutes 51.45 seconds (2691.45 seconds total)