Starting phenix.real_space_refine on Tue Feb 11 05:11:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbw_34645/02_2025/8hbw_34645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbw_34645/02_2025/8hbw_34645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hbw_34645/02_2025/8hbw_34645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbw_34645/02_2025/8hbw_34645.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbw_34645/02_2025/8hbw_34645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbw_34645/02_2025/8hbw_34645.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.159 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 18 5.16 5 C 2109 2.51 5 N 548 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2179 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'ATP': 1, 'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 3.08, per 1000 atoms: 0.93 Number of scatterers: 3309 At special positions: 0 Unit cell: (65.052, 71.724, 111.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 7 15.00 O 627 8.00 N 548 7.00 C 2109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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: 0.93 Conformation dependent library (CDL) restraints added in 397.5 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 62.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 11 through 42 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 76 through 94 removed outlier: 4.367A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 111 through 143 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 167 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.629A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 204 Processing helix chain 'A' and resid 210 through 242 removed outlier: 4.224A pdb=" N HIS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.609A pdb=" N SER A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.892A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.892A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 627 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: 1.06 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 547 1.32 - 1.44: 902 1.44 - 1.56: 1893 1.56 - 1.68: 13 1.68 - 1.81: 27 Bond restraints: 3382 Sorted by residual: bond pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.446 -0.112 1.10e-02 8.26e+03 1.03e+02 bond pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.454 -0.112 1.50e-02 4.44e+03 5.57e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.43e+01 bond pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.449 -0.107 1.50e-02 4.44e+03 5.10e+01 ... (remaining 3377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 4506 3.41 - 6.82: 70 6.82 - 10.22: 14 10.22 - 13.63: 1 13.63 - 17.04: 1 Bond angle restraints: 4592 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 124.25 12.58 1.00e+00 1.00e+00 1.58e+02 angle pdb=" C5 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N3 ATP A 401 " ideal model delta sigma weight residual 126.80 119.46 7.34 1.00e+00 1.00e+00 5.39e+01 angle pdb=" C11 CDL A 402 " pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.23 -8.90 1.32e+00 5.72e-01 4.53e+01 angle pdb=" N3 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 127.04 134.51 -7.47 1.15e+00 7.59e-01 4.24e+01 ... (remaining 4587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 1792 17.12 - 34.24: 156 34.24 - 51.36: 64 51.36 - 68.49: 14 68.49 - 85.61: 6 Dihedral angle restraints: 2032 sinusoidal: 849 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ALA A 208 " pdb=" C ALA A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 209 " pdb=" C ASP A 209 " pdb=" N ASP A 210 " pdb=" CA ASP A 210 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB GLU A 100 " pdb=" CG GLU A 100 " pdb=" CD GLU A 100 " pdb=" OE1 GLU A 100 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 3.00e+01 1.11e-03 9.85e+00 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 331 0.043 - 0.086: 138 0.086 - 0.129: 33 0.129 - 0.172: 5 0.172 - 0.214: 3 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA LYS A 66 " pdb=" N LYS A 66 " pdb=" C LYS A 66 " pdb=" CB LYS A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 261 " pdb=" N GLU A 261 " pdb=" C GLU A 261 " pdb=" CB GLU A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA ARG A 238 " pdb=" N ARG A 238 " pdb=" C ARG A 238 " pdb=" CB ARG A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 507 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 9 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO A 10 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 84 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C GLN A 84 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN A 84 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 85 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 101 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C PHE B 101 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE B 101 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY B 102 " -0.010 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 360 2.74 - 3.28: 3189 3.28 - 3.82: 5979 3.82 - 4.36: 7174 4.36 - 4.90: 12102 Nonbonded interactions: 28804 Sorted by model distance: nonbonded pdb=" OG1 THR A 103 " pdb=" O THR A 108 " model vdw 2.199 3.040 nonbonded pdb=" OE2 GLU A 45 " pdb=" OH TYR A 247 " model vdw 2.266 3.040 nonbonded pdb=" O LYS A 292 " pdb=" OG SER A 296 " model vdw 2.276 3.040 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.320 3.040 nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.323 3.040 ... (remaining 28799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.990 Find NCS groups from input model: 0.030 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.010 0.124 3382 Z= 0.670 Angle : 1.053 17.042 4592 Z= 0.645 Chirality : 0.050 0.214 510 Planarity : 0.005 0.057 567 Dihedral : 16.265 85.607 1275 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.39), residues: 410 helix: 1.83 (0.32), residues: 221 sheet: -0.32 (0.61), residues: 60 loop : 0.59 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 173 HIS 0.003 0.001 HIS B 124 PHE 0.018 0.003 PHE A 223 TYR 0.014 0.002 TYR A 157 ARG 0.021 0.002 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.407 Fit side-chains REVERT: A 55 LYS cc_start: 0.8108 (tttp) cc_final: 0.7810 (tptp) REVERT: A 161 ARG cc_start: 0.7447 (ttt180) cc_final: 0.6715 (mtt90) REVERT: A 206 ILE cc_start: 0.6885 (mm) cc_final: 0.6564 (mp) REVERT: A 248 LYS cc_start: 0.8664 (ptmm) cc_final: 0.8426 (ptmt) REVERT: A 293 ARG cc_start: 0.6520 (ptm-80) cc_final: 0.6132 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 1.5253 time to fit residues: 96.8858 Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.134402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120193 restraints weight = 3547.180| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 0.87 r_work: 0.3230 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3382 Z= 0.211 Angle : 0.537 6.816 4592 Z= 0.284 Chirality : 0.040 0.139 510 Planarity : 0.005 0.051 567 Dihedral : 13.653 78.242 569 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.48 % Allowed : 9.20 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.40), residues: 410 helix: 2.66 (0.32), residues: 221 sheet: 0.05 (0.65), residues: 54 loop : 0.65 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS A 145 PHE 0.009 0.002 PHE A 223 TYR 0.008 0.001 TYR A 74 ARG 0.005 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.364 Fit side-chains REVERT: A 55 LYS cc_start: 0.8311 (tttp) cc_final: 0.7828 (tptp) REVERT: A 117 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7632 (tt) REVERT: A 161 ARG cc_start: 0.7950 (ttt180) cc_final: 0.6632 (mtt90) REVERT: A 206 ILE cc_start: 0.6782 (mm) cc_final: 0.6410 (mp) REVERT: A 293 ARG cc_start: 0.6406 (ptm-80) cc_final: 0.6011 (tmt-80) outliers start: 5 outliers final: 0 residues processed: 63 average time/residue: 1.3541 time to fit residues: 87.6389 Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.116363 restraints weight = 3575.346| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.94 r_work: 0.3170 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3382 Z= 0.299 Angle : 0.577 7.393 4592 Z= 0.301 Chirality : 0.042 0.140 510 Planarity : 0.005 0.046 567 Dihedral : 13.350 74.782 569 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.37 % Allowed : 11.57 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.40), residues: 410 helix: 2.75 (0.32), residues: 221 sheet: -0.05 (0.64), residues: 54 loop : 0.59 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.002 0.001 HIS B 124 PHE 0.016 0.002 PHE A 223 TYR 0.010 0.001 TYR A 157 ARG 0.005 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.382 Fit side-chains REVERT: A 55 LYS cc_start: 0.8380 (tttp) cc_final: 0.7873 (tptp) REVERT: A 57 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8205 (t) REVERT: A 117 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7654 (tt) REVERT: A 161 ARG cc_start: 0.8006 (ttt180) cc_final: 0.6617 (mtt90) REVERT: A 206 ILE cc_start: 0.6874 (mm) cc_final: 0.6506 (mp) REVERT: A 293 ARG cc_start: 0.6415 (ptm-80) cc_final: 0.6046 (tmt-80) outliers start: 8 outliers final: 3 residues processed: 58 average time/residue: 1.3771 time to fit residues: 82.1154 Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.131453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.116521 restraints weight = 3653.675| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 0.95 r_work: 0.3169 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3382 Z= 0.287 Angle : 0.572 7.899 4592 Z= 0.297 Chirality : 0.042 0.140 510 Planarity : 0.005 0.043 567 Dihedral : 13.180 74.324 569 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.37 % Allowed : 13.06 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.40), residues: 410 helix: 2.79 (0.32), residues: 221 sheet: -0.07 (0.64), residues: 54 loop : 0.62 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.002 0.001 HIS A 147 PHE 0.015 0.002 PHE A 223 TYR 0.010 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.361 Fit side-chains REVERT: A 55 LYS cc_start: 0.8385 (tttp) cc_final: 0.7885 (tptp) REVERT: A 57 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8197 (t) REVERT: A 117 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7671 (tt) REVERT: A 161 ARG cc_start: 0.8041 (ttt180) cc_final: 0.6671 (mtt90) REVERT: A 206 ILE cc_start: 0.6842 (mm) cc_final: 0.6481 (mp) REVERT: A 293 ARG cc_start: 0.6497 (ptm-80) cc_final: 0.6120 (tmt-80) outliers start: 8 outliers final: 3 residues processed: 58 average time/residue: 1.3915 time to fit residues: 83.0062 Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 20 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.137272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122604 restraints weight = 3569.544| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 0.90 r_work: 0.3257 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 3382 Z= 0.156 Angle : 0.504 8.511 4592 Z= 0.258 Chirality : 0.039 0.138 510 Planarity : 0.004 0.041 567 Dihedral : 12.033 70.480 569 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.08 % Allowed : 13.65 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.40), residues: 410 helix: 3.07 (0.33), residues: 221 sheet: 0.13 (0.66), residues: 54 loop : 0.69 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.002 0.000 HIS A 145 PHE 0.006 0.001 PHE A 128 TYR 0.006 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.363 Fit side-chains REVERT: A 53 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7464 (tmt170) REVERT: A 55 LYS cc_start: 0.8307 (tttp) cc_final: 0.7808 (tptp) REVERT: A 57 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8153 (t) REVERT: A 70 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6696 (ptt90) REVERT: A 117 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7594 (tt) REVERT: A 161 ARG cc_start: 0.7980 (ttt180) cc_final: 0.6610 (mtt90) REVERT: A 206 ILE cc_start: 0.6414 (mm) cc_final: 0.6085 (mp) REVERT: A 293 ARG cc_start: 0.6439 (ptm-80) cc_final: 0.6070 (tmt-80) outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 1.2771 time to fit residues: 81.4289 Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.137817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122004 restraints weight = 3806.326| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.08 r_work: 0.3257 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3382 Z= 0.182 Angle : 0.513 8.285 4592 Z= 0.264 Chirality : 0.039 0.125 510 Planarity : 0.004 0.039 567 Dihedral : 11.879 70.333 569 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.08 % Allowed : 14.84 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.41), residues: 410 helix: 3.10 (0.33), residues: 222 sheet: 0.30 (0.68), residues: 54 loop : 0.82 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 57 HIS 0.001 0.001 HIS A 145 PHE 0.011 0.001 PHE B 101 TYR 0.008 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.417 Fit side-chains REVERT: A 53 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7573 (tmt170) REVERT: A 55 LYS cc_start: 0.8349 (tttp) cc_final: 0.7855 (tptp) REVERT: A 57 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8160 (t) REVERT: A 70 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6537 (mtp-110) REVERT: A 117 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7672 (tt) REVERT: A 161 ARG cc_start: 0.8059 (ttt180) cc_final: 0.6712 (mtt90) REVERT: A 206 ILE cc_start: 0.6521 (mm) cc_final: 0.6200 (mp) REVERT: A 293 ARG cc_start: 0.6478 (ptm-80) cc_final: 0.6120 (tmt-80) outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 1.2895 time to fit residues: 82.2044 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120824 restraints weight = 3701.355| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.06 r_work: 0.3233 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3382 Z= 0.222 Angle : 0.541 8.265 4592 Z= 0.280 Chirality : 0.040 0.125 510 Planarity : 0.005 0.038 567 Dihedral : 12.089 71.648 569 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.37 % Allowed : 15.13 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.40), residues: 410 helix: 3.06 (0.32), residues: 222 sheet: 0.19 (0.68), residues: 54 loop : 0.78 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 105 HIS 0.002 0.001 HIS A 147 PHE 0.012 0.002 PHE B 101 TYR 0.009 0.001 TYR A 157 ARG 0.004 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.377 Fit side-chains REVERT: A 53 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7563 (tmt170) REVERT: A 55 LYS cc_start: 0.8385 (tttp) cc_final: 0.7901 (tptp) REVERT: A 57 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8173 (t) REVERT: A 70 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6597 (mtp-110) REVERT: A 117 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 161 ARG cc_start: 0.8042 (ttt180) cc_final: 0.6698 (mtt90) REVERT: A 206 ILE cc_start: 0.6591 (mm) cc_final: 0.6263 (mp) REVERT: A 293 ARG cc_start: 0.6552 (ptm-80) cc_final: 0.6156 (tmt-80) outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 1.3397 time to fit residues: 83.9402 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.137483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121623 restraints weight = 3547.763| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.07 r_work: 0.3223 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3382 Z= 0.171 Angle : 0.513 8.709 4592 Z= 0.263 Chirality : 0.039 0.123 510 Planarity : 0.004 0.037 567 Dihedral : 11.600 70.295 569 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.08 % Allowed : 15.13 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.40), residues: 410 helix: 3.13 (0.33), residues: 223 sheet: 0.33 (0.69), residues: 54 loop : 0.85 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.001 0.000 HIS A 145 PHE 0.010 0.001 PHE B 101 TYR 0.007 0.001 TYR A 157 ARG 0.003 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.324 Fit side-chains REVERT: A 53 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7554 (tmt170) REVERT: A 55 LYS cc_start: 0.8341 (tttp) cc_final: 0.7819 (tptp) REVERT: A 70 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6546 (mtp-110) REVERT: A 117 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7604 (tt) REVERT: A 161 ARG cc_start: 0.8036 (ttt180) cc_final: 0.6595 (mtt90) REVERT: A 206 ILE cc_start: 0.6397 (mm) cc_final: 0.6077 (mp) REVERT: A 293 ARG cc_start: 0.6435 (ptm-80) cc_final: 0.6081 (tmt-80) outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 1.3064 time to fit residues: 84.5238 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.138655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122911 restraints weight = 3679.940| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.06 r_work: 0.3260 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3382 Z= 0.181 Angle : 0.519 8.694 4592 Z= 0.267 Chirality : 0.039 0.124 510 Planarity : 0.004 0.037 567 Dihedral : 11.504 70.271 569 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.37 % Allowed : 15.43 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.40), residues: 410 helix: 3.14 (0.33), residues: 223 sheet: 0.28 (0.69), residues: 54 loop : 0.88 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.001 0.000 HIS A 145 PHE 0.010 0.002 PHE B 101 TYR 0.008 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.352 Fit side-chains REVERT: A 53 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7573 (tmt170) REVERT: A 55 LYS cc_start: 0.8361 (tttp) cc_final: 0.7874 (tptp) REVERT: A 70 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6561 (mtp-110) REVERT: A 117 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 161 ARG cc_start: 0.8031 (ttt180) cc_final: 0.6696 (mtt90) REVERT: A 206 ILE cc_start: 0.6484 (mm) cc_final: 0.6261 (mp) REVERT: A 293 ARG cc_start: 0.6498 (ptm-80) cc_final: 0.6140 (tmt-80) outliers start: 8 outliers final: 3 residues processed: 60 average time/residue: 1.3208 time to fit residues: 81.4433 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.0020 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122659 restraints weight = 3681.282| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.05 r_work: 0.3257 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3382 Z= 0.192 Angle : 0.527 8.812 4592 Z= 0.272 Chirality : 0.039 0.125 510 Planarity : 0.004 0.037 567 Dihedral : 11.521 70.566 569 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.67 % Allowed : 15.13 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.41), residues: 410 helix: 3.18 (0.32), residues: 222 sheet: 0.22 (0.70), residues: 54 loop : 0.82 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 103 HIS 0.001 0.000 HIS A 147 PHE 0.009 0.001 PHE A 223 TYR 0.008 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.389 Fit side-chains REVERT: A 53 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7558 (tmt170) REVERT: A 55 LYS cc_start: 0.8379 (tttp) cc_final: 0.7883 (tptp) REVERT: A 66 LYS cc_start: 0.7753 (mmpt) cc_final: 0.7299 (mmmt) REVERT: A 70 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6561 (mtp-110) REVERT: A 117 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7685 (tt) REVERT: A 161 ARG cc_start: 0.8043 (ttt180) cc_final: 0.6712 (mtt90) REVERT: A 206 ILE cc_start: 0.6498 (mm) cc_final: 0.6277 (mp) REVERT: A 293 ARG cc_start: 0.6486 (ptm-80) cc_final: 0.6129 (tmt-80) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 1.3050 time to fit residues: 83.4191 Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.121223 restraints weight = 3708.815| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.07 r_work: 0.3230 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3382 Z= 0.217 Angle : 0.540 8.671 4592 Z= 0.279 Chirality : 0.040 0.128 510 Planarity : 0.004 0.037 567 Dihedral : 11.779 71.265 569 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.37 % Allowed : 15.43 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.40), residues: 410 helix: 3.12 (0.32), residues: 222 sheet: 0.26 (0.70), residues: 54 loop : 0.82 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 105 HIS 0.002 0.001 HIS A 147 PHE 0.011 0.002 PHE A 223 TYR 0.009 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3098.85 seconds wall clock time: 55 minutes 15.42 seconds (3315.42 seconds total)