Starting phenix.real_space_refine on Wed Mar 5 21:14:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0m_26944/03_2025/7v0m_26944.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0m_26944/03_2025/7v0m_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_26944/03_2025/7v0m_26944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0m_26944/03_2025/7v0m_26944.map" model { file = "/net/cci-nas-00/data/ceres_data/7v0m_26944/03_2025/7v0m_26944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0m_26944/03_2025/7v0m_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-5624/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: 3.19, per 1000 atoms: 0.86 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: 0.95 Conformation dependent library (CDL) restraints added in 443.9 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: 0.37 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: 0.92 Time building geometry restraints manager: 1.12 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: 1.230 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.880 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.070 ------------------------------------------------------------------------------- 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 : 0.352 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: 1.2723 time to fit residues: 91.8868 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 : 0.403 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.127171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.108389 restraints weight = 4013.599| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.32 r_work: 0.2929 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 : 0.399 Fit side-chains REVERT: A 66 HIS cc_start: 0.8334 (m170) cc_final: 0.8014 (m-70) REVERT: A 187 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7108 (mtp85) outliers start: 11 outliers final: 2 residues processed: 68 average time/residue: 1.2644 time to fit residues: 88.6956 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 : 0.393 ------------------------------------------------------------------------------- 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 11 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.124043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.104324 restraints weight = 3978.756| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.39 r_work: 0.2861 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3726 Z= 0.218 Angle : 0.470 5.118 5061 Z= 0.244 Chirality : 0.040 0.123 597 Planarity : 0.004 0.033 668 Dihedral : 4.126 20.454 509 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.69 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: 1.54 (0.37), residues: 479 helix: 1.54 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.06 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 383 PHE 0.013 0.001 PHE A 234 TYR 0.007 0.002 TYR A 100 ARG 0.001 0.000 ARG A 95 *********************** 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 76 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.463 Fit side-chains REVERT: A 187 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7384 (mtp85) REVERT: A 454 LYS cc_start: 0.8647 (tttp) cc_final: 0.7674 (ttmp) REVERT: A 458 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6978 (mt0) outliers start: 14 outliers final: 5 residues processed: 71 average time/residue: 1.2361 time to fit residues: 90.7425 Evaluate side-chains 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 458 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 5 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 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 = 0.3280 r_free = 0.3280 target = 0.125251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.105622 restraints weight = 3986.278| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.39 r_work: 0.2878 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3726 Z= 0.161 Angle : 0.435 5.089 5061 Z= 0.225 Chirality : 0.038 0.122 597 Planarity : 0.004 0.034 668 Dihedral : 3.935 19.606 509 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: 1.76 (0.38), residues: 479 helix: 1.71 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.11 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 383 PHE 0.010 0.001 PHE A 234 TYR 0.007 0.001 TYR A 100 ARG 0.001 0.000 ARG A 95 *********************** 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 73 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.403 Fit side-chains REVERT: A 66 HIS cc_start: 0.8441 (m170) cc_final: 0.8122 (m-70) REVERT: A 187 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7153 (mtp85) REVERT: A 266 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7129 (pp20) outliers start: 13 outliers final: 5 residues processed: 66 average time/residue: 1.3134 time to fit residues: 89.3590 Evaluate side-chains 65 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 266 GLU 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 14 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.0000 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.128102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.109180 restraints weight = 4118.919| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.34 r_work: 0.2938 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1186 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= 0.114 Angle : 0.404 5.966 5061 Z= 0.206 Chirality : 0.036 0.120 597 Planarity : 0.004 0.034 668 Dihedral : 3.605 17.470 509 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.10 % Allowed : 17.57 % 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: 1.99 (0.38), residues: 479 helix: 1.91 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.16 (0.50), 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 216 ARG 0.001 0.000 ARG A 256 *********************** 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 78 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8696 (m-40) cc_final: 0.8469 (m-40) REVERT: A 187 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7300 (mtp85) outliers start: 12 outliers final: 6 residues processed: 72 average time/residue: 1.2274 time to fit residues: 91.4879 Evaluate side-chains 69 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 435 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 chunk 46 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.128167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.109099 restraints weight = 4089.880| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.34 r_work: 0.2931 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1242 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= 0.119 Angle : 0.411 5.486 5061 Z= 0.210 Chirality : 0.036 0.118 597 Planarity : 0.004 0.034 668 Dihedral : 3.577 16.795 509 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.36 % Allowed : 17.05 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.38), residues: 479 helix: 1.94 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.25 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.007 0.001 PHE A 234 TYR 0.005 0.001 TYR A 100 ARG 0.004 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 75 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.449 Fit side-chains REVERT: A 79 ASN cc_start: 0.8707 (m-40) cc_final: 0.8473 (m-40) REVERT: A 187 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7265 (mtp85) REVERT: A 454 LYS cc_start: 0.8517 (tttp) cc_final: 0.7228 (ttmp) REVERT: A 458 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6629 (mp10) outliers start: 13 outliers final: 5 residues processed: 69 average time/residue: 1.2440 time to fit residues: 88.6569 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 : 0.436 ------------------------------------------------------------------------------- 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 17 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.128134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.109233 restraints weight = 4034.714| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.31 r_work: 0.2924 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1242 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= 0.128 Angle : 0.422 6.327 5061 Z= 0.215 Chirality : 0.036 0.118 597 Planarity : 0.004 0.034 668 Dihedral : 3.603 16.463 509 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.36 % Allowed : 17.05 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.38), residues: 479 helix: 1.95 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.30 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.007 0.001 PHE A 234 TYR 0.005 0.001 TYR A 100 ARG 0.003 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.439 Fit side-chains REVERT: A 79 ASN cc_start: 0.8733 (m-40) cc_final: 0.8489 (m-40) REVERT: A 187 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7307 (mtp85) REVERT: A 458 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6714 (mp10) outliers start: 13 outliers final: 7 residues processed: 68 average time/residue: 1.2794 time to fit residues: 89.7660 Evaluate side-chains 69 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 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 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 458 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.128734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.109742 restraints weight = 4085.702| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.33 r_work: 0.2936 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3726 Z= 0.124 Angle : 0.426 6.602 5061 Z= 0.217 Chirality : 0.036 0.117 597 Planarity : 0.004 0.034 668 Dihedral : 3.568 16.234 509 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: 2.12 (0.38), residues: 479 helix: 1.95 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.35 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.006 0.001 PHE A 234 TYR 0.005 0.001 TYR A 216 ARG 0.004 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.408 Fit side-chains REVERT: A 79 ASN cc_start: 0.8718 (m-40) cc_final: 0.8471 (m-40) REVERT: A 187 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7309 (mtp85) REVERT: A 454 LYS cc_start: 0.8541 (tttp) cc_final: 0.7592 (ttmp) REVERT: W 22 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7046 (pt0) outliers start: 13 outliers final: 6 residues processed: 69 average time/residue: 1.2192 time to fit residues: 86.8280 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.126693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.107568 restraints weight = 4015.464| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.32 r_work: 0.2910 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1249 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= 0.148 Angle : 0.449 6.758 5061 Z= 0.229 Chirality : 0.037 0.116 597 Planarity : 0.004 0.034 668 Dihedral : 3.692 16.766 509 Min Nonbonded Distance : 2.641 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: 2.03 (0.38), residues: 479 helix: 1.86 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.37 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 383 PHE 0.008 0.001 PHE A 234 TYR 0.009 0.001 TYR A 455 ARG 0.004 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.422 Fit side-chains REVERT: A 187 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7346 (mtp85) REVERT: A 458 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6616 (mp10) REVERT: W 22 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7070 (pt0) outliers start: 12 outliers final: 5 residues processed: 66 average time/residue: 1.2203 time to fit residues: 83.2414 Evaluate side-chains 65 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- 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 = 0.3286 r_free = 0.3286 target = 0.125891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.105948 restraints weight = 4037.580| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.40 r_work: 0.2886 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1155 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= 0.171 Angle : 0.470 6.875 5061 Z= 0.240 Chirality : 0.038 0.116 597 Planarity : 0.004 0.034 668 Dihedral : 3.812 17.600 509 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.33 % Allowed : 18.86 % 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: 1.96 (0.38), residues: 479 helix: 1.81 (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 162 PHE 0.009 0.001 PHE A 234 TYR 0.007 0.001 TYR A 100 ARG 0.004 0.000 ARG A 426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.441 Fit side-chains REVERT: A 187 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7378 (mtp85) REVERT: A 454 LYS cc_start: 0.8551 (tttp) cc_final: 0.7610 (ttmp) outliers start: 9 outliers final: 5 residues processed: 62 average time/residue: 1.3470 time to fit residues: 86.2693 Evaluate side-chains 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.127730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.108244 restraints weight = 3990.945| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.37 r_work: 0.2887 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1163 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= 0.171 Angle : 0.472 6.876 5061 Z= 0.241 Chirality : 0.038 0.116 597 Planarity : 0.004 0.034 668 Dihedral : 3.844 18.029 509 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.07 % Allowed : 18.86 % 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: 1.94 (0.38), residues: 479 helix: 1.78 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.36 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.010 0.001 PHE A 234 TYR 0.007 0.001 TYR A 100 ARG 0.004 0.000 ARG A 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4169.42 seconds wall clock time: 71 minutes 49.73 seconds (4309.73 seconds total)