Starting phenix.real_space_refine on Wed Sep 17 03:15:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3l_44144/09_2025/9b3l_44144_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3l_44144/09_2025/9b3l_44144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b3l_44144/09_2025/9b3l_44144_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3l_44144/09_2025/9b3l_44144_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b3l_44144/09_2025/9b3l_44144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3l_44144/09_2025/9b3l_44144.map" } resolution = 3.25 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= 0.037 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 1768 2.51 5 N 407 2.21 5 O 433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 2623 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2623 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 12, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 0.93, per 1000 atoms: 0.35 Number of scatterers: 2623 At special positions: 0 Unit cell: (59.4, 70.95, 80.025, 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 433 8.00 N 407 7.00 C 1768 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: 0.21 Conformation dependent library (CDL) restraints added in 144.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 644 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 removed outlier: 3.871A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 4.047A pdb=" N LYS A 31 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 removed outlier: 3.887A pdb=" N LEU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Proline residue: A 56 - end of helix removed outlier: 3.638A pdb=" N LYS A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 88 Processing helix chain 'A' and resid 90 through 120 Proline residue: A 110 - end of helix removed outlier: 3.588A pdb=" N ALA A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 151 removed outlier: 3.630A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 156 through 175 removed outlier: 3.842A pdb=" N TYR A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 232 removed outlier: 3.630A pdb=" N PHE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 261 Processing helix chain 'A' and resid 267 through 288 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 303 through 321 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 326 through 354 Proline residue: A 344 - end of helix removed outlier: 3.667A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 390 233 hydrogen bonds defined for protein. 699 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: 0.52 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 776 1.34 - 1.46: 581 1.46 - 1.58: 1301 1.58 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 2687 Sorted by residual: bond pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.94e-01 bond pdb=" CB ASP A 385 " pdb=" CG ASP A 385 " ideal model delta sigma weight residual 1.516 1.533 -0.017 2.50e-02 1.60e+03 4.77e-01 bond pdb=" CA ASN A 319 " pdb=" CB ASN A 319 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.66e-02 3.63e+03 4.30e-01 bond pdb=" CG PRO A 24 " pdb=" CD PRO A 24 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.28e-01 bond pdb=" C MET A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 4.06e-01 ... (remaining 2682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 3491 1.12 - 2.23: 127 2.23 - 3.35: 16 3.35 - 4.47: 6 4.47 - 5.58: 8 Bond angle restraints: 3648 Sorted by residual: angle pdb=" N PHE A 259 " pdb=" CA PHE A 259 " pdb=" C PHE A 259 " ideal model delta sigma weight residual 112.90 109.93 2.97 1.31e+00 5.83e-01 5.13e+00 angle pdb=" C TYR A 257 " pdb=" N PHE A 258 " pdb=" CA PHE A 258 " ideal model delta sigma weight residual 122.31 118.74 3.57 2.00e+00 2.50e-01 3.19e+00 angle pdb=" CA ASN A 319 " pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " ideal model delta sigma weight residual 112.60 114.33 -1.73 1.00e+00 1.00e+00 2.98e+00 angle pdb=" N VAL A 302 " pdb=" CA VAL A 302 " pdb=" C VAL A 302 " ideal model delta sigma weight residual 113.16 110.61 2.55 1.49e+00 4.50e-01 2.92e+00 angle pdb=" CA ASP A 385 " pdb=" CB ASP A 385 " pdb=" CG ASP A 385 " ideal model delta sigma weight residual 112.60 114.30 -1.70 1.00e+00 1.00e+00 2.90e+00 ... (remaining 3643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 1219 11.94 - 23.89: 182 23.89 - 35.83: 79 35.83 - 47.77: 35 47.77 - 59.71: 9 Dihedral angle restraints: 1524 sinusoidal: 514 harmonic: 1010 Sorted by residual: dihedral pdb=" CA PHE A 259 " pdb=" C PHE A 259 " pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" N ASN A 137 " pdb=" CA ASN A 137 " pdb=" CB ASN A 137 " pdb=" CG ASN A 137 " ideal model delta sinusoidal sigma weight residual -60.00 -119.71 59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ILE A 346 " pdb=" CB ILE A 346 " pdb=" CG1 ILE A 346 " pdb=" CD1 ILE A 346 " ideal model delta sinusoidal sigma weight residual 60.00 115.94 -55.94 3 1.50e+01 4.44e-03 9.37e+00 ... (remaining 1521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 253 0.027 - 0.054: 95 0.054 - 0.081: 57 0.081 - 0.108: 25 0.108 - 0.134: 4 Chirality restraints: 434 Sorted by residual: chirality pdb=" CA THR A 206 " pdb=" N THR A 206 " pdb=" C THR A 206 " pdb=" CB THR A 206 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CG LEU A 165 " pdb=" CB LEU A 165 " pdb=" CD1 LEU A 165 " pdb=" CD2 LEU A 165 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA PRO A 344 " pdb=" N PRO A 344 " pdb=" C PRO A 344 " pdb=" CB PRO A 344 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 431 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 27 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 343 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 344 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 256 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ILE A 256 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE A 256 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR A 257 " 0.008 2.00e-02 2.50e+03 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 734 2.80 - 3.32: 2727 3.32 - 3.85: 4553 3.85 - 4.37: 4861 4.37 - 4.90: 8619 Nonbonded interactions: 21494 Sorted by model distance: nonbonded pdb=" NZ LYS A 232 " pdb=" O ALA A 289 " model vdw 2.274 3.120 nonbonded pdb=" O SER A 241 " pdb=" OG1 THR A 245 " model vdw 2.304 3.040 nonbonded pdb=" O SER A 122 " pdb=" NZ LYS A 125 " model vdw 2.309 3.120 nonbonded pdb=" OD1 ASP A 385 " pdb=" N LEU A 386 " model vdw 2.442 3.120 nonbonded pdb=" OG SER A 133 " pdb=" OG1 THR A 314 " model vdw 2.463 3.040 ... (remaining 21489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.950 Find NCS groups from input model: 0.010 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 0.022 2687 Z= 0.139 Angle : 0.537 5.582 3648 Z= 0.286 Chirality : 0.040 0.134 434 Planarity : 0.005 0.053 445 Dihedral : 15.962 59.714 880 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.40 % Allowed : 32.41 % Favored : 67.19 % 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: 2.14 (0.46), residues: 350 helix: 2.04 (0.30), residues: 302 sheet: None (None), residues: 0 loop : -2.80 (0.84), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.011 0.001 TYR A 228 PHE 0.012 0.001 PHE A 216 TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2687) covalent geometry : angle 0.53683 ( 3648) hydrogen bonds : bond 0.12448 ( 233) hydrogen bonds : angle 5.08984 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.096 Fit side-chains REVERT: A 156 ARG cc_start: 0.6516 (ttm-80) cc_final: 0.6315 (ttm-80) REVERT: A 338 MET cc_start: 0.8799 (ttm) cc_final: 0.8526 (ttp) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.0471 time to fit residues: 4.2443 Evaluate side-chains 69 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0060 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.167556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135499 restraints weight = 3600.035| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.96 r_work: 0.3449 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2687 Z= 0.126 Angle : 0.495 5.578 3648 Z= 0.263 Chirality : 0.040 0.124 434 Planarity : 0.005 0.051 445 Dihedral : 4.071 18.570 372 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.14 % Allowed : 28.46 % Favored : 66.40 % 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: 2.61 (0.45), residues: 350 helix: 2.27 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.64 (0.91), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.010 0.001 TYR A 360 PHE 0.012 0.001 PHE A 335 TRP 0.005 0.000 TRP A 293 HIS 0.001 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2687) covalent geometry : angle 0.49457 ( 3648) hydrogen bonds : bond 0.03773 ( 233) hydrogen bonds : angle 4.01684 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.095 Fit side-chains REVERT: A 64 LYS cc_start: 0.4950 (OUTLIER) cc_final: 0.4711 (tptm) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.0473 time to fit residues: 4.5086 Evaluate side-chains 80 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 320 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.166703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134655 restraints weight = 3657.751| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.96 r_work: 0.3428 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2687 Z= 0.137 Angle : 0.493 5.446 3648 Z= 0.262 Chirality : 0.040 0.117 434 Planarity : 0.004 0.048 445 Dihedral : 4.079 19.705 370 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 6.72 % Allowed : 26.09 % Favored : 67.19 % 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: 2.69 (0.45), residues: 350 helix: 2.32 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.56 (0.91), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.012 0.001 TYR A 360 PHE 0.013 0.001 PHE A 335 TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 2687) covalent geometry : angle 0.49337 ( 3648) hydrogen bonds : bond 0.03557 ( 233) hydrogen bonds : angle 3.93995 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.104 Fit side-chains REVERT: A 64 LYS cc_start: 0.4886 (OUTLIER) cc_final: 0.4647 (tptm) REVERT: A 160 TYR cc_start: 0.7753 (m-80) cc_final: 0.7501 (m-80) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.0382 time to fit residues: 3.9474 Evaluate side-chains 76 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.165930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133706 restraints weight = 3607.777| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.96 r_work: 0.3410 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2687 Z= 0.145 Angle : 0.527 6.953 3648 Z= 0.271 Chirality : 0.041 0.125 434 Planarity : 0.004 0.046 445 Dihedral : 4.137 19.691 370 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 6.72 % Allowed : 27.67 % Favored : 65.61 % 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: 2.63 (0.46), residues: 350 helix: 2.28 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.57 (0.93), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.020 0.002 TYR A 225 PHE 0.014 0.001 PHE A 159 TRP 0.004 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 2687) covalent geometry : angle 0.52657 ( 3648) hydrogen bonds : bond 0.03594 ( 233) hydrogen bonds : angle 3.95316 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.098 Fit side-chains REVERT: A 64 LYS cc_start: 0.4798 (OUTLIER) cc_final: 0.4520 (tptm) REVERT: A 156 ARG cc_start: 0.6622 (ttm-80) cc_final: 0.6388 (ttm-80) REVERT: A 295 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7794 (tt) REVERT: A 338 MET cc_start: 0.8862 (ttm) cc_final: 0.8660 (ttp) outliers start: 17 outliers final: 13 residues processed: 78 average time/residue: 0.0500 time to fit residues: 4.8562 Evaluate side-chains 79 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 0.0070 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.167072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134993 restraints weight = 3575.602| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.93 r_work: 0.3429 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2687 Z= 0.128 Angle : 0.525 6.438 3648 Z= 0.264 Chirality : 0.041 0.150 434 Planarity : 0.004 0.045 445 Dihedral : 4.105 20.546 370 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.93 % Allowed : 28.06 % Favored : 66.01 % 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: 2.77 (0.46), residues: 350 helix: 2.37 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.40 (0.92), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 380 TYR 0.017 0.001 TYR A 225 PHE 0.012 0.001 PHE A 335 TRP 0.004 0.000 TRP A 293 HIS 0.001 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 2687) covalent geometry : angle 0.52464 ( 3648) hydrogen bonds : bond 0.03402 ( 233) hydrogen bonds : angle 3.88661 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.070 Fit side-chains REVERT: A 64 LYS cc_start: 0.4930 (OUTLIER) cc_final: 0.4617 (tptm) REVERT: A 160 TYR cc_start: 0.7755 (m-80) cc_final: 0.7494 (m-80) REVERT: A 338 MET cc_start: 0.8844 (ttm) cc_final: 0.8592 (ttp) REVERT: A 341 PHE cc_start: 0.7628 (t80) cc_final: 0.7380 (t80) REVERT: A 342 ILE cc_start: 0.8794 (mm) cc_final: 0.8589 (mt) outliers start: 15 outliers final: 13 residues processed: 84 average time/residue: 0.0438 time to fit residues: 4.6169 Evaluate side-chains 83 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.164226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131562 restraints weight = 3583.353| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.03 r_work: 0.3383 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2687 Z= 0.162 Angle : 0.549 5.637 3648 Z= 0.280 Chirality : 0.042 0.123 434 Planarity : 0.004 0.044 445 Dihedral : 4.152 20.392 370 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 6.32 % Allowed : 28.85 % Favored : 64.82 % 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: 2.57 (0.45), residues: 350 helix: 2.23 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.42 (0.90), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 380 TYR 0.013 0.002 TYR A 225 PHE 0.016 0.002 PHE A 159 TRP 0.004 0.001 TRP A 293 HIS 0.001 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 2687) covalent geometry : angle 0.54943 ( 3648) hydrogen bonds : bond 0.03726 ( 233) hydrogen bonds : angle 3.98798 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.098 Fit side-chains REVERT: A 64 LYS cc_start: 0.4897 (OUTLIER) cc_final: 0.4576 (tptm) REVERT: A 295 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7819 (tt) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.0506 time to fit residues: 4.8273 Evaluate side-chains 76 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 0.0870 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133981 restraints weight = 3581.459| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.96 r_work: 0.3418 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2687 Z= 0.133 Angle : 0.540 6.098 3648 Z= 0.274 Chirality : 0.041 0.122 434 Planarity : 0.004 0.043 445 Dihedral : 4.121 20.759 370 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 6.72 % Allowed : 28.85 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.69 (0.46), residues: 350 helix: 2.30 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.30 (0.90), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 156 TYR 0.013 0.001 TYR A 225 PHE 0.013 0.001 PHE A 159 TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2687) covalent geometry : angle 0.53952 ( 3648) hydrogen bonds : bond 0.03506 ( 233) hydrogen bonds : angle 3.93339 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.105 Fit side-chains REVERT: A 64 LYS cc_start: 0.4805 (OUTLIER) cc_final: 0.4486 (tptm) REVERT: A 71 ILE cc_start: 0.8302 (mp) cc_final: 0.7819 (mt) REVERT: A 160 TYR cc_start: 0.7807 (m-80) cc_final: 0.7534 (m-80) REVERT: A 295 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7808 (tt) REVERT: A 341 PHE cc_start: 0.7639 (t80) cc_final: 0.7280 (t80) outliers start: 17 outliers final: 13 residues processed: 79 average time/residue: 0.0531 time to fit residues: 5.1716 Evaluate side-chains 81 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.165472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132917 restraints weight = 3640.793| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.01 r_work: 0.3393 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2687 Z= 0.151 Angle : 0.567 6.325 3648 Z= 0.286 Chirality : 0.041 0.132 434 Planarity : 0.004 0.042 445 Dihedral : 4.177 20.486 370 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 6.32 % Allowed : 30.43 % Favored : 63.24 % 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: 2.58 (0.45), residues: 350 helix: 2.24 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -2.31 (0.85), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 156 TYR 0.011 0.001 TYR A 225 PHE 0.016 0.001 PHE A 159 TRP 0.004 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2687) covalent geometry : angle 0.56726 ( 3648) hydrogen bonds : bond 0.03673 ( 233) hydrogen bonds : angle 4.02189 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.095 Fit side-chains REVERT: A 31 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7747 (mttp) REVERT: A 64 LYS cc_start: 0.4834 (OUTLIER) cc_final: 0.4487 (tptm) REVERT: A 71 ILE cc_start: 0.8329 (mp) cc_final: 0.7792 (mt) REVERT: A 295 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7809 (tt) outliers start: 16 outliers final: 12 residues processed: 79 average time/residue: 0.0593 time to fit residues: 5.6692 Evaluate side-chains 80 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.165423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133668 restraints weight = 3628.763| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.95 r_work: 0.3402 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2687 Z= 0.150 Angle : 0.578 6.604 3648 Z= 0.290 Chirality : 0.042 0.128 434 Planarity : 0.004 0.042 445 Dihedral : 4.205 20.440 370 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.53 % Allowed : 31.23 % Favored : 63.24 % 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: 2.53 (0.45), residues: 350 helix: 2.20 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -2.29 (0.84), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 156 TYR 0.010 0.001 TYR A 160 PHE 0.015 0.001 PHE A 159 TRP 0.004 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2687) covalent geometry : angle 0.57823 ( 3648) hydrogen bonds : bond 0.03714 ( 233) hydrogen bonds : angle 4.04258 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.099 Fit side-chains REVERT: A 31 LYS cc_start: 0.8391 (mmmt) cc_final: 0.7777 (mttp) REVERT: A 49 LEU cc_start: 0.8245 (tt) cc_final: 0.8043 (tp) REVERT: A 64 LYS cc_start: 0.4835 (OUTLIER) cc_final: 0.4478 (tptm) REVERT: A 71 ILE cc_start: 0.8343 (mp) cc_final: 0.7787 (mt) outliers start: 14 outliers final: 11 residues processed: 78 average time/residue: 0.0638 time to fit residues: 5.9728 Evaluate side-chains 78 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.164893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132375 restraints weight = 3665.079| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.02 r_work: 0.3386 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2687 Z= 0.168 Angle : 0.611 6.928 3648 Z= 0.305 Chirality : 0.043 0.130 434 Planarity : 0.004 0.042 445 Dihedral : 4.298 20.265 370 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.93 % Allowed : 31.62 % Favored : 62.45 % 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: 2.37 (0.45), residues: 350 helix: 2.07 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.24 (0.85), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 380 TYR 0.011 0.001 TYR A 160 PHE 0.017 0.002 PHE A 159 TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 2687) covalent geometry : angle 0.61083 ( 3648) hydrogen bonds : bond 0.03859 ( 233) hydrogen bonds : angle 4.13208 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.075 Fit side-chains REVERT: A 31 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7770 (mttp) REVERT: A 49 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7986 (tp) REVERT: A 64 LYS cc_start: 0.4827 (OUTLIER) cc_final: 0.4493 (tptm) REVERT: A 71 ILE cc_start: 0.8350 (mp) cc_final: 0.7910 (mt) REVERT: A 376 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8385 (tm-30) outliers start: 15 outliers final: 11 residues processed: 78 average time/residue: 0.0620 time to fit residues: 5.8062 Evaluate side-chains 78 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.165767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134027 restraints weight = 3617.346| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.95 r_work: 0.3397 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2687 Z= 0.154 Angle : 0.607 8.217 3648 Z= 0.303 Chirality : 0.043 0.143 434 Planarity : 0.004 0.042 445 Dihedral : 4.376 20.516 370 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.93 % Allowed : 31.62 % Favored : 62.45 % 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: 2.33 (0.45), residues: 350 helix: 2.03 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.21 (0.85), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 156 TYR 0.011 0.001 TYR A 160 PHE 0.015 0.002 PHE A 341 TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 2687) covalent geometry : angle 0.60664 ( 3648) hydrogen bonds : bond 0.03787 ( 233) hydrogen bonds : angle 4.14271 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 825.19 seconds wall clock time: 14 minutes 51.72 seconds (891.72 seconds total)