Starting phenix.real_space_refine on Wed Sep 17 04:22:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9w_51159/09_2025/9g9w_51159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9w_51159/09_2025/9g9w_51159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g9w_51159/09_2025/9g9w_51159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9w_51159/09_2025/9g9w_51159.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9w_51159/09_2025/9g9w_51159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9w_51159/09_2025/9g9w_51159.cif" } resolution = 2.48 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= 0.001 sd= 0.048 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 K 3 8.98 5 S 32 5.16 5 C 2732 2.51 5 N 616 2.21 5 O 706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4089 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1938 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 253} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 8, 'GLU:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 108 Unusual residues: {' K': 3, 'Y01': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Restraints were copied for chains: B Time building chain proxies: 1.61, per 1000 atoms: 0.39 Number of scatterers: 4089 At special positions: 0 Unit cell: (60.736, 80.704, 94.848, 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) K 3 19.00 S 32 16.00 O 706 8.00 N 616 7.00 C 2732 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: 0.42 Conformation dependent library (CDL) restraints added in 102.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.573A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 Proline residue: A 71 - end of helix removed outlier: 3.979A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 removed outlier: 3.675A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 182 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 248 removed outlier: 5.290A pdb=" N ARG A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'B' and resid 3 through 53 removed outlier: 5.573A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 74 Proline residue: B 71 - end of helix removed outlier: 3.980A pdb=" N ALA B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 removed outlier: 3.675A pdb=" N LEU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 182 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 248 removed outlier: 5.290A pdb=" N ARG B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 343 hydrogen bonds defined for protein. 1029 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: 0.70 Time building geometry restraints manager: 0.53 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: 632 1.32 - 1.44: 1134 1.44 - 1.56: 2376 1.56 - 1.68: 0 1.68 - 1.81: 50 Bond restraints: 4192 Sorted by residual: bond pdb=" CAL Y01 A 302 " pdb=" CAX Y01 A 302 " ideal model delta sigma weight residual 1.540 1.513 0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CAL Y01 B 302 " pdb=" CAX Y01 B 302 " ideal model delta sigma weight residual 1.540 1.514 0.026 2.00e-02 2.50e+03 1.64e+00 bond pdb=" CAL Y01 B 303 " pdb=" CAX Y01 B 303 " ideal model delta sigma weight residual 1.540 1.515 0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CAL Y01 A 303 " pdb=" CAX Y01 A 303 " ideal model delta sigma weight residual 1.540 1.515 0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CAL Y01 B 301 " pdb=" CAX Y01 B 301 " ideal model delta sigma weight residual 1.540 1.516 0.024 2.00e-02 2.50e+03 1.48e+00 ... (remaining 4187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 4931 0.95 - 1.90: 653 1.90 - 2.86: 94 2.86 - 3.81: 34 3.81 - 4.76: 18 Bond angle restraints: 5730 Sorted by residual: angle pdb=" N SER B 31 " pdb=" CA SER B 31 " pdb=" C SER B 31 " ideal model delta sigma weight residual 111.82 115.38 -3.56 1.16e+00 7.43e-01 9.41e+00 angle pdb=" N SER A 31 " pdb=" CA SER A 31 " pdb=" C SER A 31 " ideal model delta sigma weight residual 111.82 115.34 -3.52 1.16e+00 7.43e-01 9.22e+00 angle pdb=" CA TYR A 96 " pdb=" CB TYR A 96 " pdb=" CG TYR A 96 " ideal model delta sigma weight residual 113.90 118.00 -4.10 1.80e+00 3.09e-01 5.20e+00 angle pdb=" CA TYR B 96 " pdb=" CB TYR B 96 " pdb=" CG TYR B 96 " ideal model delta sigma weight residual 113.90 117.99 -4.09 1.80e+00 3.09e-01 5.16e+00 angle pdb=" N PHE A 80 " pdb=" CA PHE A 80 " pdb=" C PHE A 80 " ideal model delta sigma weight residual 111.11 113.66 -2.55 1.20e+00 6.94e-01 4.53e+00 ... (remaining 5725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 2486 15.06 - 30.13: 160 30.13 - 45.19: 34 45.19 - 60.25: 20 60.25 - 75.31: 2 Dihedral angle restraints: 2702 sinusoidal: 1202 harmonic: 1500 Sorted by residual: dihedral pdb=" CA LYS B 79 " pdb=" C LYS B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LYS A 79 " pdb=" C LYS A 79 " pdb=" N PHE A 80 " pdb=" CA PHE A 80 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA HIS A 98 " pdb=" C HIS A 98 " pdb=" N ALA A 99 " pdb=" CA ALA A 99 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 2699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 341 0.034 - 0.068: 253 0.068 - 0.103: 60 0.103 - 0.137: 22 0.137 - 0.171: 6 Chirality restraints: 682 Sorted by residual: chirality pdb=" CA LEU A 208 " pdb=" N LEU A 208 " pdb=" C LEU A 208 " pdb=" CB LEU A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA LEU B 208 " pdb=" N LEU B 208 " pdb=" C LEU B 208 " pdb=" CB LEU B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA TRP B 78 " pdb=" N TRP B 78 " pdb=" C TRP B 78 " pdb=" CB TRP B 78 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 679 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 137 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C ARG B 137 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG B 137 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR B 138 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 137 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C ARG A 137 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG A 137 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 138 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 39 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C GLU A 39 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU A 39 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 40 " -0.012 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 1394 2.86 - 3.43: 4737 3.43 - 4.00: 7582 4.00 - 4.57: 11233 4.57 - 5.14: 15661 Nonbonded interactions: 40607 Sorted by model distance: nonbonded pdb=" OE2 GLU A 182 " pdb=" OH TYR A 220 " model vdw 2.295 3.040 nonbonded pdb=" OE2 GLU B 182 " pdb=" OH TYR B 220 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.301 3.040 nonbonded pdb=" OD2 ASP A 58 " pdb=" OH TYR B 52 " model vdw 2.301 3.040 nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.420 3.040 ... (remaining 40602 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 303) selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.610 Find NCS groups from input model: 0.070 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:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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 : 0.007 0.044 4192 Z= 0.300 Angle : 0.724 4.758 5730 Z= 0.446 Chirality : 0.050 0.171 682 Planarity : 0.006 0.022 680 Dihedral : 11.378 75.314 1742 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.33), residues: 512 helix: 0.52 (0.22), residues: 420 sheet: None (None), residues: 0 loop : 0.25 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 236 TYR 0.022 0.005 TYR A 96 PHE 0.026 0.002 PHE B 202 TRP 0.018 0.003 TRP B 78 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00723 ( 4192) covalent geometry : angle 0.72426 ( 5730) hydrogen bonds : bond 0.10702 ( 343) hydrogen bonds : angle 4.90247 ( 1029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.156 Fit side-chains REVERT: A 3 ARG cc_start: 0.5993 (ttt180) cc_final: 0.5750 (ttt-90) REVERT: A 47 ARG cc_start: 0.6227 (ttt-90) cc_final: 0.5936 (ttp80) REVERT: A 135 PHE cc_start: 0.7716 (t80) cc_final: 0.7422 (t80) REVERT: A 137 ARG cc_start: 0.6533 (ttm-80) cc_final: 0.6138 (ttp-170) REVERT: B 3 ARG cc_start: 0.6007 (ttt180) cc_final: 0.5762 (ttt-90) REVERT: B 47 ARG cc_start: 0.6222 (ttt-90) cc_final: 0.5931 (ttp80) REVERT: B 135 PHE cc_start: 0.7738 (t80) cc_final: 0.7445 (t80) REVERT: B 137 ARG cc_start: 0.6552 (ttm-80) cc_final: 0.6154 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.6859 time to fit residues: 48.0281 Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.0270 chunk 22 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104336 restraints weight = 4610.318| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.66 r_work: 0.2975 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4192 Z= 0.118 Angle : 0.431 4.807 5730 Z= 0.240 Chirality : 0.037 0.128 682 Planarity : 0.003 0.029 680 Dihedral : 7.363 53.034 978 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.53 % Allowed : 6.35 % Favored : 93.12 % 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: 3.83 (0.35), residues: 512 helix: 2.94 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.48 (0.68), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 131 TYR 0.012 0.002 TYR A 96 PHE 0.017 0.001 PHE A 109 TRP 0.013 0.002 TRP B 78 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4192) covalent geometry : angle 0.43138 ( 5730) hydrogen bonds : bond 0.04385 ( 343) hydrogen bonds : angle 3.42398 ( 1029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.131 Fit side-chains REVERT: A 3 ARG cc_start: 0.6256 (ttt180) cc_final: 0.5969 (ttt-90) REVERT: A 135 PHE cc_start: 0.7862 (t80) cc_final: 0.7525 (t80) REVERT: A 137 ARG cc_start: 0.6326 (ttm-80) cc_final: 0.6022 (ttp-170) REVERT: B 3 ARG cc_start: 0.6258 (ttt180) cc_final: 0.5979 (ttt-90) REVERT: B 135 PHE cc_start: 0.7864 (t80) cc_final: 0.7525 (t80) REVERT: B 137 ARG cc_start: 0.6312 (ttm-80) cc_final: 0.6009 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.7870 time to fit residues: 50.0455 Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.0670 chunk 49 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101480 restraints weight = 4568.827| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.66 r_work: 0.2934 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4192 Z= 0.148 Angle : 0.444 5.020 5730 Z= 0.246 Chirality : 0.037 0.133 682 Planarity : 0.003 0.026 680 Dihedral : 7.194 52.757 978 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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: 4.23 (0.36), residues: 512 helix: 3.29 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.24 (0.67), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 47 TYR 0.014 0.002 TYR A 96 PHE 0.016 0.001 PHE A 109 TRP 0.011 0.002 TRP B 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4192) covalent geometry : angle 0.44438 ( 5730) hydrogen bonds : bond 0.04779 ( 343) hydrogen bonds : angle 3.37086 ( 1029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.151 Fit side-chains REVERT: A 3 ARG cc_start: 0.6382 (ttt180) cc_final: 0.6041 (ttt-90) REVERT: A 51 LYS cc_start: 0.6665 (tttt) cc_final: 0.6412 (tttt) REVERT: A 135 PHE cc_start: 0.7867 (t80) cc_final: 0.7586 (t80) REVERT: A 137 ARG cc_start: 0.6353 (ttm-80) cc_final: 0.6010 (ttp-170) REVERT: B 3 ARG cc_start: 0.6358 (ttt180) cc_final: 0.5986 (ttt-90) REVERT: B 51 LYS cc_start: 0.6662 (tttt) cc_final: 0.6409 (tttt) REVERT: B 135 PHE cc_start: 0.7865 (t80) cc_final: 0.7582 (t80) REVERT: B 137 ARG cc_start: 0.6346 (ttm-80) cc_final: 0.6003 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 64 average time/residue: 0.8117 time to fit residues: 53.1807 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099395 restraints weight = 4519.456| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.63 r_work: 0.2915 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4192 Z= 0.172 Angle : 0.462 5.091 5730 Z= 0.254 Chirality : 0.038 0.138 682 Planarity : 0.003 0.025 680 Dihedral : 7.180 53.358 978 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % 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: 4.42 (0.36), residues: 512 helix: 3.39 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.76 (0.70), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 236 TYR 0.014 0.002 TYR A 96 PHE 0.016 0.002 PHE B 109 TRP 0.008 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 4192) covalent geometry : angle 0.46182 ( 5730) hydrogen bonds : bond 0.05061 ( 343) hydrogen bonds : angle 3.37737 ( 1029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.180 Fit side-chains REVERT: A 3 ARG cc_start: 0.6356 (ttt180) cc_final: 0.6015 (ttt-90) REVERT: A 51 LYS cc_start: 0.6627 (tttt) cc_final: 0.6393 (tttt) REVERT: A 135 PHE cc_start: 0.7821 (t80) cc_final: 0.7497 (t80) REVERT: A 137 ARG cc_start: 0.6269 (ttm-80) cc_final: 0.5924 (ttp-170) REVERT: B 3 ARG cc_start: 0.6368 (ttt180) cc_final: 0.6027 (ttt-90) REVERT: B 51 LYS cc_start: 0.6617 (tttt) cc_final: 0.6383 (tttt) REVERT: B 135 PHE cc_start: 0.7819 (t80) cc_final: 0.7495 (t80) REVERT: B 137 ARG cc_start: 0.6254 (ttm-80) cc_final: 0.5912 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.8217 time to fit residues: 52.2091 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101124 restraints weight = 4515.866| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.65 r_work: 0.2927 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4192 Z= 0.151 Angle : 0.439 5.107 5730 Z= 0.242 Chirality : 0.037 0.132 682 Planarity : 0.002 0.023 680 Dihedral : 7.063 54.835 978 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % 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: 4.52 (0.36), residues: 512 helix: 3.46 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.79 (0.72), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 47 TYR 0.012 0.002 TYR B 96 PHE 0.015 0.001 PHE B 109 TRP 0.006 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4192) covalent geometry : angle 0.43851 ( 5730) hydrogen bonds : bond 0.04744 ( 343) hydrogen bonds : angle 3.30338 ( 1029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.153 Fit side-chains REVERT: A 3 ARG cc_start: 0.6415 (ttt180) cc_final: 0.6023 (ttt-90) REVERT: A 135 PHE cc_start: 0.7838 (t80) cc_final: 0.7555 (t80) REVERT: A 137 ARG cc_start: 0.6302 (ttm-80) cc_final: 0.5954 (ttp-170) REVERT: B 3 ARG cc_start: 0.6405 (ttt180) cc_final: 0.6071 (ttt-90) REVERT: B 135 PHE cc_start: 0.7838 (t80) cc_final: 0.7553 (t80) REVERT: B 137 ARG cc_start: 0.6285 (ttm-80) cc_final: 0.5940 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.7648 time to fit residues: 48.5653 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102400 restraints weight = 4621.574| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.68 r_work: 0.3118 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4192 Z= 0.125 Angle : 0.410 5.112 5730 Z= 0.226 Chirality : 0.036 0.125 682 Planarity : 0.002 0.022 680 Dihedral : 6.903 56.993 978 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.53 % Allowed : 11.11 % Favored : 88.36 % 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: 4.66 (0.36), residues: 512 helix: 3.55 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 0.81 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 47 TYR 0.011 0.001 TYR A 96 PHE 0.015 0.001 PHE A 109 TRP 0.006 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4192) covalent geometry : angle 0.41001 ( 5730) hydrogen bonds : bond 0.04308 ( 343) hydrogen bonds : angle 3.22285 ( 1029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.152 Fit side-chains REVERT: A 3 ARG cc_start: 0.6478 (ttt180) cc_final: 0.6080 (ttt-90) REVERT: A 135 PHE cc_start: 0.7928 (t80) cc_final: 0.7583 (t80) REVERT: A 137 ARG cc_start: 0.6392 (ttm-80) cc_final: 0.6031 (ttp-170) REVERT: B 3 ARG cc_start: 0.6510 (ttt180) cc_final: 0.6182 (ttt-90) REVERT: B 47 ARG cc_start: 0.6568 (ttt-90) cc_final: 0.6103 (ttp80) REVERT: B 135 PHE cc_start: 0.7933 (t80) cc_final: 0.7592 (t80) REVERT: B 137 ARG cc_start: 0.6390 (ttm-80) cc_final: 0.6030 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.8487 time to fit residues: 53.9059 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.0070 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100949 restraints weight = 4594.532| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.67 r_work: 0.3122 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4192 Z= 0.155 Angle : 0.444 5.141 5730 Z= 0.243 Chirality : 0.037 0.134 682 Planarity : 0.002 0.022 680 Dihedral : 7.007 57.833 978 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.53 % Allowed : 11.64 % Favored : 87.83 % 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: 4.54 (0.36), residues: 512 helix: 3.51 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.62 (0.67), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 47 TYR 0.011 0.001 TYR B 96 PHE 0.015 0.001 PHE B 109 TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4192) covalent geometry : angle 0.44402 ( 5730) hydrogen bonds : bond 0.04757 ( 343) hydrogen bonds : angle 3.29936 ( 1029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.155 Fit side-chains REVERT: A 3 ARG cc_start: 0.6578 (ttt180) cc_final: 0.6183 (ttt-90) REVERT: A 47 ARG cc_start: 0.6802 (ttt-90) cc_final: 0.6303 (ttp80) REVERT: A 135 PHE cc_start: 0.7986 (t80) cc_final: 0.7713 (t80) REVERT: A 137 ARG cc_start: 0.6506 (ttm-80) cc_final: 0.6123 (ttp-170) REVERT: B 3 ARG cc_start: 0.6622 (ttt180) cc_final: 0.6279 (ttt-90) REVERT: B 47 ARG cc_start: 0.6723 (ttt-90) cc_final: 0.6253 (ttp80) REVERT: B 135 PHE cc_start: 0.7994 (t80) cc_final: 0.7717 (t80) REVERT: B 137 ARG cc_start: 0.6510 (ttm-80) cc_final: 0.6128 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.8542 time to fit residues: 54.2645 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.0000 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104136 restraints weight = 4478.446| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.64 r_work: 0.2973 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4192 Z= 0.107 Angle : 0.390 5.072 5730 Z= 0.215 Chirality : 0.035 0.120 682 Planarity : 0.002 0.021 680 Dihedral : 6.788 59.884 978 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % 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: 4.77 (0.36), residues: 512 helix: 3.65 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 0.71 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 236 TYR 0.010 0.001 TYR B 96 PHE 0.014 0.001 PHE B 109 TRP 0.006 0.001 TRP A 78 HIS 0.000 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 4192) covalent geometry : angle 0.38987 ( 5730) hydrogen bonds : bond 0.03982 ( 343) hydrogen bonds : angle 3.15494 ( 1029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.156 Fit side-chains REVERT: A 3 ARG cc_start: 0.6320 (ttt180) cc_final: 0.5940 (ttt-90) REVERT: A 135 PHE cc_start: 0.7821 (t80) cc_final: 0.7489 (t80) REVERT: A 137 ARG cc_start: 0.6244 (ttm-80) cc_final: 0.5905 (ttp-170) REVERT: B 3 ARG cc_start: 0.6357 (ttt180) cc_final: 0.6030 (ttt-90) REVERT: B 135 PHE cc_start: 0.7818 (t80) cc_final: 0.7488 (t80) REVERT: B 137 ARG cc_start: 0.6238 (ttm-80) cc_final: 0.5899 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 56 average time/residue: 0.7740 time to fit residues: 44.4292 Evaluate side-chains 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 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 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102720 restraints weight = 4584.047| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.67 r_work: 0.2941 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4192 Z= 0.123 Angle : 0.412 5.134 5730 Z= 0.225 Chirality : 0.035 0.126 682 Planarity : 0.002 0.021 680 Dihedral : 6.761 58.773 978 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % 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: 4.76 (0.36), residues: 512 helix: 3.63 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 0.78 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.010 0.001 TYR A 96 PHE 0.014 0.001 PHE A 109 TRP 0.005 0.001 TRP B 78 HIS 0.000 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4192) covalent geometry : angle 0.41231 ( 5730) hydrogen bonds : bond 0.04233 ( 343) hydrogen bonds : angle 3.19880 ( 1029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.188 Fit side-chains REVERT: A 3 ARG cc_start: 0.6350 (ttt180) cc_final: 0.5967 (ttt-90) REVERT: A 135 PHE cc_start: 0.7851 (t80) cc_final: 0.7523 (t80) REVERT: A 137 ARG cc_start: 0.6212 (ttm-80) cc_final: 0.5861 (ttp-170) REVERT: B 3 ARG cc_start: 0.6402 (ttt180) cc_final: 0.6072 (ttt-90) REVERT: B 135 PHE cc_start: 0.7848 (t80) cc_final: 0.7522 (t80) REVERT: B 137 ARG cc_start: 0.6204 (ttm-80) cc_final: 0.5854 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 56 average time/residue: 0.8218 time to fit residues: 47.2777 Evaluate side-chains 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101387 restraints weight = 4486.158| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.65 r_work: 0.2919 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4192 Z= 0.147 Angle : 0.439 5.163 5730 Z= 0.239 Chirality : 0.037 0.132 682 Planarity : 0.002 0.022 680 Dihedral : 6.933 58.762 978 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % 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: 4.64 (0.36), residues: 512 helix: 3.53 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 0.82 (0.67), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 47 TYR 0.010 0.001 TYR A 96 PHE 0.015 0.001 PHE A 109 TRP 0.004 0.001 TRP A 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4192) covalent geometry : angle 0.43855 ( 5730) hydrogen bonds : bond 0.04634 ( 343) hydrogen bonds : angle 3.26557 ( 1029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.168 Fit side-chains REVERT: A 3 ARG cc_start: 0.6374 (ttt180) cc_final: 0.5987 (ttt-90) REVERT: A 135 PHE cc_start: 0.7849 (t80) cc_final: 0.7583 (t80) REVERT: A 137 ARG cc_start: 0.6281 (ttm-80) cc_final: 0.5920 (ttp-170) REVERT: B 3 ARG cc_start: 0.6408 (ttt180) cc_final: 0.6078 (ttt-90) REVERT: B 135 PHE cc_start: 0.7845 (t80) cc_final: 0.7578 (t80) REVERT: B 137 ARG cc_start: 0.6273 (ttm-80) cc_final: 0.5919 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.8809 time to fit residues: 55.9580 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104037 restraints weight = 4510.979| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.67 r_work: 0.2967 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4192 Z= 0.111 Angle : 0.400 5.114 5730 Z= 0.218 Chirality : 0.035 0.120 682 Planarity : 0.002 0.021 680 Dihedral : 6.706 57.086 978 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % 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: 4.79 (0.36), residues: 512 helix: 3.64 (0.24), residues: 414 sheet: None (None), residues: 0 loop : 0.87 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 47 TYR 0.010 0.001 TYR A 96 PHE 0.014 0.001 PHE A 109 TRP 0.005 0.001 TRP B 78 HIS 0.000 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 4192) covalent geometry : angle 0.40037 ( 5730) hydrogen bonds : bond 0.04006 ( 343) hydrogen bonds : angle 3.16549 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2076.98 seconds wall clock time: 36 minutes 8.03 seconds (2168.03 seconds total)