Starting phenix.real_space_refine on Wed Sep 17 04:01:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0m_26944/09_2025/7v0m_26944.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0m_26944/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v0m_26944/09_2025/7v0m_26944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0m_26944/09_2025/7v0m_26944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v0m_26944/09_2025/7v0m_26944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0m_26944/09_2025/7v0m_26944.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'GLN:plan1': 2, '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: 1.34, per 1000 atoms: 0.36 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: 0.40 Conformation dependent library (CDL) restraints added in 181.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.13 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: 0.57 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1285 1.34 - 1.46: 646 1.46 - 1.58: 1770 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 3726 Sorted by residual: bond pdb=" CB LYS A 270 " pdb=" CG LYS A 270 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.93e-01 bond pdb=" CG LYS A 270 " pdb=" CD LYS A 270 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.12e-01 bond pdb=" CG1 ILE A 38 " pdb=" CD1 ILE A 38 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.55e-01 bond pdb=" CB ASN A 434 " pdb=" CG ASN A 434 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.02e-01 bond pdb=" CB VAL A 410 " pdb=" CG1 VAL A 410 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.92e-01 ... (remaining 3721 not shown) Histogram of bond angle deviations from ideal: 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: 2.220 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: 0.300 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.200 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:9.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.270 ------------------------------------------------------------------------------- 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= 0.142 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 95 TYR 0.013 0.002 TYR A 455 PHE 0.011 0.001 PHE A 234 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3726) covalent geometry : angle 0.56286 ( 5061) hydrogen bonds : bond 0.15194 ( 187) hydrogen bonds : angle 4.65837 ( 555) *********************** 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 : 0.210 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: 0.6329 time to fit residues: 45.5563 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 : 0.152 ------------------------------------------------------------------------------- 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 24 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 0.0570 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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 W 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.123071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.103285 restraints weight = 4046.092| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.41 r_work: 0.2845 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3726 Z= 0.149 Angle : 0.487 5.098 5061 Z= 0.254 Chirality : 0.040 0.126 597 Planarity : 0.004 0.035 668 Dihedral : 6.250 87.276 514 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.88 % Allowed : 16.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.37), residues: 479 helix: 1.32 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.02 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.008 0.002 TYR A 100 PHE 0.013 0.001 PHE A 234 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3726) covalent geometry : angle 0.48673 ( 5061) hydrogen bonds : bond 0.04252 ( 187) hydrogen bonds : angle 3.95663 ( 555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.156 Fit side-chains REVERT: A 66 HIS cc_start: 0.8445 (m170) cc_final: 0.8113 (m-70) REVERT: A 187 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7157 (mtp85) outliers start: 15 outliers final: 4 residues processed: 69 average time/residue: 0.6014 time to fit residues: 42.7694 Evaluate side-chains 68 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.124635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.104911 restraints weight = 3968.479| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.39 r_work: 0.2874 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3726 Z= 0.114 Angle : 0.446 5.109 5061 Z= 0.232 Chirality : 0.038 0.124 597 Planarity : 0.004 0.033 668 Dihedral : 4.062 20.404 509 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.37), residues: 479 helix: 1.57 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.05 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 95 TYR 0.007 0.001 TYR A 100 PHE 0.011 0.001 PHE A 234 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3726) covalent geometry : angle 0.44650 ( 5061) hydrogen bonds : bond 0.03582 ( 187) hydrogen bonds : angle 3.75105 ( 555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.177 Fit side-chains REVERT: A 187 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7389 (mtp85) REVERT: A 454 LYS cc_start: 0.8562 (tttp) cc_final: 0.8021 (tptp) outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 0.6106 time to fit residues: 45.2652 Evaluate side-chains 66 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.125533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.105984 restraints weight = 3999.822| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.39 r_work: 0.2881 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0986 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= 0.100 Angle : 0.431 5.064 5061 Z= 0.223 Chirality : 0.038 0.123 597 Planarity : 0.004 0.034 668 Dihedral : 3.916 19.525 509 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.39 % Allowed : 16.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (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 ARG 0.001 0.000 ARG A 95 TYR 0.009 0.001 TYR A 455 PHE 0.010 0.001 PHE A 234 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3726) covalent geometry : angle 0.43102 ( 5061) hydrogen bonds : bond 0.03207 ( 187) hydrogen bonds : angle 3.63996 ( 555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8439 (m170) cc_final: 0.8114 (m-70) REVERT: A 185 ASP cc_start: 0.8134 (t0) cc_final: 0.7913 (t0) REVERT: A 187 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7128 (mtp85) REVERT: A 266 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7127 (pp20) outliers start: 17 outliers final: 7 residues processed: 70 average time/residue: 0.6372 time to fit residues: 45.8955 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 : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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 266 GLU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain W residue 31 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.0070 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.125619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.106358 restraints weight = 4033.668| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.37 r_work: 0.2899 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3726 Z= 0.105 Angle : 0.437 5.113 5061 Z= 0.225 Chirality : 0.038 0.122 597 Planarity : 0.004 0.035 668 Dihedral : 3.922 19.224 509 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.65 % Allowed : 16.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.38), residues: 479 helix: 1.72 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.17 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 426 TYR 0.006 0.001 TYR A 100 PHE 0.010 0.001 PHE A 234 HIS 0.002 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3726) covalent geometry : angle 0.43664 ( 5061) hydrogen bonds : bond 0.03269 ( 187) hydrogen bonds : angle 3.64367 ( 555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.180 Fit side-chains REVERT: A 66 HIS cc_start: 0.8461 (m170) cc_final: 0.8120 (m-70) REVERT: A 185 ASP cc_start: 0.8098 (t0) cc_final: 0.7867 (t0) REVERT: A 187 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7095 (mtp85) REVERT: A 266 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7101 (pp20) REVERT: A 454 LYS cc_start: 0.8479 (tttp) cc_final: 0.7524 (ttmp) REVERT: A 458 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6657 (mp10) outliers start: 18 outliers final: 9 residues processed: 71 average time/residue: 0.6236 time to fit residues: 45.5726 Evaluate side-chains 72 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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 266 GLU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 31 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.126643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.107080 restraints weight = 4044.826| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.40 r_work: 0.2895 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1109 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= 0.087 Angle : 0.416 5.082 5061 Z= 0.214 Chirality : 0.037 0.121 597 Planarity : 0.004 0.035 668 Dihedral : 3.755 18.314 509 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.91 % Allowed : 16.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.38), residues: 479 helix: 1.83 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.22 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 426 TYR 0.006 0.001 TYR A 100 PHE 0.008 0.001 PHE A 234 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 3726) covalent geometry : angle 0.41592 ( 5061) hydrogen bonds : bond 0.02860 ( 187) hydrogen bonds : angle 3.51154 ( 555) *********************** 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 80 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.093 Fit side-chains REVERT: A 185 ASP cc_start: 0.8003 (t0) cc_final: 0.7737 (t0) REVERT: A 187 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7361 (mtp85) REVERT: A 266 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7059 (pp20) REVERT: A 454 LYS cc_start: 0.8450 (tttp) cc_final: 0.7478 (ttmp) REVERT: A 458 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6620 (mp10) outliers start: 19 outliers final: 9 residues processed: 72 average time/residue: 0.5951 time to fit residues: 44.0915 Evaluate side-chains 70 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain W residue 13 GLU Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 31 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.127795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.108056 restraints weight = 4092.644| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.42 r_work: 0.2910 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1245 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= 0.081 Angle : 0.414 6.462 5061 Z= 0.211 Chirality : 0.036 0.120 597 Planarity : 0.004 0.035 668 Dihedral : 3.628 17.199 509 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.91 % Allowed : 16.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.38), residues: 479 helix: 1.91 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.26 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 426 TYR 0.005 0.001 TYR A 216 PHE 0.007 0.001 PHE A 234 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 3726) covalent geometry : angle 0.41397 ( 5061) hydrogen bonds : bond 0.02676 ( 187) hydrogen bonds : angle 3.43849 ( 555) *********************** 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 84 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.173 Fit side-chains REVERT: A 79 ASN cc_start: 0.8747 (m-40) cc_final: 0.8510 (m-40) REVERT: A 185 ASP cc_start: 0.7914 (t0) cc_final: 0.7619 (t0) REVERT: A 187 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7296 (mtp85) REVERT: A 401 THR cc_start: 0.8425 (p) cc_final: 0.8184 (p) REVERT: A 454 LYS cc_start: 0.8430 (tttp) cc_final: 0.7496 (ttmp) REVERT: A 458 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6660 (mp10) outliers start: 19 outliers final: 10 residues processed: 77 average time/residue: 0.6024 time to fit residues: 47.7739 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 : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain W residue 31 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.0020 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.123677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.103987 restraints weight = 4065.363| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.40 r_work: 0.2847 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3726 Z= 0.144 Angle : 0.488 5.483 5061 Z= 0.250 Chirality : 0.040 0.119 597 Planarity : 0.004 0.036 668 Dihedral : 4.057 19.574 509 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.13 % Allowed : 16.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.38), residues: 479 helix: 1.73 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.19 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.015 0.002 TYR A 455 PHE 0.013 0.001 PHE A 234 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3726) covalent geometry : angle 0.48772 ( 5061) hydrogen bonds : bond 0.03764 ( 187) hydrogen bonds : angle 3.72909 ( 555) *********************** 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 81 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.169 Fit side-chains REVERT: A 66 HIS cc_start: 0.8476 (m170) cc_final: 0.8133 (m-70) REVERT: A 185 ASP cc_start: 0.8198 (t0) cc_final: 0.7967 (t0) REVERT: A 187 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7151 (mtp85) REVERT: A 454 LYS cc_start: 0.8518 (tttp) cc_final: 0.7509 (ttmp) REVERT: A 458 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6716 (mp10) outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 0.5716 time to fit residues: 44.2660 Evaluate side-chains 70 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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 31 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.127645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.108451 restraints weight = 4021.741| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.38 r_work: 0.2890 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1157 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= 0.093 Angle : 0.432 5.379 5061 Z= 0.222 Chirality : 0.037 0.119 597 Planarity : 0.004 0.036 668 Dihedral : 3.806 18.413 509 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.84 % Allowed : 18.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.38), residues: 479 helix: 1.87 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.23 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.010 0.001 TYR A 455 PHE 0.008 0.001 PHE A 234 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 3726) covalent geometry : angle 0.43224 ( 5061) hydrogen bonds : bond 0.02965 ( 187) hydrogen bonds : angle 3.53065 ( 555) *********************** 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 72 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8044 (t0) cc_final: 0.7750 (t0) REVERT: A 187 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7333 (mtp85) REVERT: A 454 LYS cc_start: 0.8466 (tttp) cc_final: 0.7894 (ttmp) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.6069 time to fit residues: 41.9273 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 : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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 31 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 0.0000 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 183 ASN A 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.127002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.107377 restraints weight = 4084.575| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.41 r_work: 0.2900 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1222 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= 0.087 Angle : 0.431 6.883 5061 Z= 0.219 Chirality : 0.037 0.118 597 Planarity : 0.004 0.036 668 Dihedral : 3.680 17.444 509 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.58 % Allowed : 19.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.38), residues: 479 helix: 1.91 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.27 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 426 TYR 0.005 0.001 TYR A 100 PHE 0.007 0.001 PHE A 234 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 3726) covalent geometry : angle 0.43134 ( 5061) hydrogen bonds : bond 0.02790 ( 187) hydrogen bonds : angle 3.49739 ( 555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.7942 (t0) cc_final: 0.7641 (t0) REVERT: A 187 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7296 (mtp85) REVERT: A 401 THR cc_start: 0.8501 (p) cc_final: 0.8236 (p) REVERT: A 454 LYS cc_start: 0.8455 (tttp) cc_final: 0.7896 (ttmp) outliers start: 10 outliers final: 8 residues processed: 67 average time/residue: 0.6301 time to fit residues: 43.4945 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 : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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 31 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.0170 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.0050 chunk 2 optimal weight: 0.8980 overall best weight: 0.3570 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.130911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.111477 restraints weight = 3983.132| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.39 r_work: 0.2962 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3726 Z= 0.074 Angle : 0.411 7.002 5061 Z= 0.208 Chirality : 0.036 0.118 597 Planarity : 0.004 0.036 668 Dihedral : 3.446 15.568 509 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.33 % Allowed : 19.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.38), residues: 479 helix: 2.01 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.35 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 426 TYR 0.005 0.001 TYR A 100 PHE 0.005 0.001 PHE A 234 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00170 ( 3726) covalent geometry : angle 0.41138 ( 5061) hydrogen bonds : bond 0.02342 ( 187) hydrogen bonds : angle 3.31202 ( 555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.71 seconds wall clock time: 39 minutes 17.56 seconds (2357.56 seconds total)