Starting phenix.real_space_refine on Wed Jul 1 23:18:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9w_51159/07_2026/9g9w_51159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9w_51159/07_2026/9g9w_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 { model { file = "/net/cci-nas-00/data/ceres_data/9g9w_51159/07_2026/9g9w_51159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9w_51159/07_2026/9g9w_51159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g9w_51159/07_2026/9g9w_51159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9w_51159/07_2026/9g9w_51159.map" } 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4089 Number of models: 1 Model: "" Number of chains: 4 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: "B" 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, 105 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 3 Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.17, per 1000 atoms: 0.29 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: 0.35 Conformation dependent library (CDL) restraints added in 143.2 milliseconds 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: 0.08 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: 0.64 Time building geometry restraints manager: 0.47 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 5.170 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:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 are 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/Z covalent geometry : bond 0.00723 / 0.30 ( 4192) covalent geometry : angle 0.72426 / 0.45 ( 5730) hydrogen bonds : bond 0.10702 / 6.52 ( 343) hydrogen bonds : angle 4.90247 / 3.66 ( 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 : 0.087 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: 0.5602 time to fit residues: 39.2455 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 : 0.101 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 0.0270 chunk 22 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3616 r_free = 0.3616 target = 0.135223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102480 restraints weight = 4724.080| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.69 r_work: 0.2952 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4192 Z= 0.125 Angle : 0.447 4.768 5730 Z= 0.249 Chirality : 0.037 0.136 682 Planarity : 0.003 0.029 680 Dihedral : 7.485 52.286 978 Min Nonbonded Distance : 2.557 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 are not related in a simple way. whole: 3.81 (0.36), residues: 512 helix: 2.87 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.85 (0.72), 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 0.016 0.001 PHE B 109 TRP 0.013 0.002 TRP B 78 HIS 0.001 0.000 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 4192) covalent geometry : angle 0.44673 / 0.25 ( 5730) hydrogen bonds : bond 0.04568 / 3.08 ( 343) hydrogen bonds : angle 3.50501 / 2.66 ( 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 : 0.174 Fit side-chains REVERT: A 3 ARG cc_start: 0.6198 (ttt180) cc_final: 0.5926 (ttt-90) REVERT: A 135 PHE cc_start: 0.7835 (t80) cc_final: 0.7486 (t80) REVERT: A 137 ARG cc_start: 0.6261 (ttm-80) cc_final: 0.5964 (ttp-170) REVERT: B 3 ARG cc_start: 0.6202 (ttt180) cc_final: 0.5934 (ttt-90) REVERT: B 135 PHE cc_start: 0.7808 (t80) cc_final: 0.7463 (t80) REVERT: B 137 ARG cc_start: 0.6249 (ttm-80) cc_final: 0.5952 (ttp-170) outliers start: 2 outliers final: 0 residues processed: 62 average time/residue: 0.6808 time to fit residues: 43.4032 Evaluate side-chains 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3640 r_free = 0.3640 target = 0.136466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103446 restraints weight = 4616.793| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.67 r_work: 0.3131 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4192 Z= 0.125 Angle : 0.426 4.995 5730 Z= 0.236 Chirality : 0.036 0.133 682 Planarity : 0.003 0.026 680 Dihedral : 7.093 53.325 978 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.53 % Allowed : 8.99 % 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 are not related in a simple way. whole: 4.44 (0.36), residues: 512 helix: 3.37 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.69 (0.71), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 3 TYR 0.015 0.002 TYR A 96 PHE 0.016 0.001 PHE B 109 TRP 0.012 0.002 TRP B 78 HIS 0.000 0.000 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 4192) covalent geometry : angle 0.42561 / 0.24 ( 5730) hydrogen bonds : bond 0.04352 / 2.93 ( 343) hydrogen bonds : angle 3.31163 / 2.51 ( 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 66 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.180 Fit side-chains REVERT: A 3 ARG cc_start: 0.6441 (ttt180) cc_final: 0.6091 (ttt-90) REVERT: A 51 LYS cc_start: 0.6841 (tttt) cc_final: 0.6630 (tttt) REVERT: A 135 PHE cc_start: 0.7993 (t80) cc_final: 0.7644 (t80) REVERT: A 137 ARG cc_start: 0.6505 (ttm-80) cc_final: 0.6141 (ttp-170) REVERT: B 3 ARG cc_start: 0.6444 (ttt180) cc_final: 0.6132 (ttt-90) REVERT: B 51 LYS cc_start: 0.6849 (tttt) cc_final: 0.6636 (tttt) REVERT: B 135 PHE cc_start: 0.7985 (t80) cc_final: 0.7640 (t80) REVERT: B 137 ARG cc_start: 0.6487 (ttm-80) cc_final: 0.6123 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 64 average time/residue: 0.7638 time to fit residues: 50.1900 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 : 0.189 ------------------------------------------------------------------------------- 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: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3613 r_free = 0.3613 target = 0.134237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101045 restraints weight = 4496.453| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.65 r_work: 0.2929 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4192 Z= 0.165 Angle : 0.464 5.084 5730 Z= 0.254 Chirality : 0.038 0.142 682 Planarity : 0.003 0.025 680 Dihedral : 7.124 54.037 978 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.53 % Allowed : 10.58 % Favored : 88.89 % 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 are not related in a simple way. whole: 4.61 (0.36), residues: 512 helix: 3.44 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 1.25 (0.74), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 47 TYR 0.015 0.002 TYR A 96 PHE 0.016 0.002 PHE A 109 TRP 0.007 0.001 TRP B 78 HIS 0.001 0.000 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 4192) covalent geometry : angle 0.46378 / 0.25 ( 5730) hydrogen bonds : bond 0.04949 / 3.32 ( 343) hydrogen bonds : angle 3.36908 / 2.55 ( 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 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: 0.6355 (ttt180) cc_final: 0.6019 (ttt-90) REVERT: A 135 PHE cc_start: 0.7842 (t80) cc_final: 0.7510 (t80) REVERT: A 137 ARG cc_start: 0.6289 (ttm-80) cc_final: 0.5947 (ttp-170) REVERT: B 3 ARG cc_start: 0.6364 (ttt180) cc_final: 0.6021 (ttt-90) REVERT: B 135 PHE cc_start: 0.7843 (t80) cc_final: 0.7512 (t80) REVERT: B 137 ARG cc_start: 0.6281 (ttm-80) cc_final: 0.5941 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.7207 time to fit residues: 45.8200 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 : 0.145 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3627 r_free = 0.3627 target = 0.135275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102276 restraints weight = 4549.710| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.67 r_work: 0.2949 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4192 Z= 0.139 Angle : 0.432 5.102 5730 Z= 0.237 Chirality : 0.037 0.135 682 Planarity : 0.002 0.023 680 Dihedral : 6.982 55.408 978 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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 are not related in a simple way. whole: 4.76 (0.36), residues: 512 helix: 3.56 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 1.22 (0.74), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.014 0.001 TYR A 96 PHE 0.015 0.001 PHE A 109 TRP 0.007 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 4192) covalent geometry : angle 0.43190 / 0.24 ( 5730) hydrogen bonds : bond 0.04511 / 3.03 ( 343) hydrogen bonds : angle 3.29280 / 2.50 ( 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 : 0.145 Fit side-chains REVERT: A 3 ARG cc_start: 0.6350 (ttt180) cc_final: 0.6013 (ttt-90) REVERT: A 135 PHE cc_start: 0.7821 (t80) cc_final: 0.7530 (t80) REVERT: A 137 ARG cc_start: 0.6271 (ttm-80) cc_final: 0.5930 (ttp-170) REVERT: B 3 ARG cc_start: 0.6352 (ttt180) cc_final: 0.6012 (ttt-90) REVERT: B 135 PHE cc_start: 0.7820 (t80) cc_final: 0.7529 (t80) REVERT: B 137 ARG cc_start: 0.6266 (ttm-80) cc_final: 0.5927 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.7214 time to fit residues: 45.9220 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 : 0.142 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.136193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103133 restraints weight = 4660.836| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.68 r_work: 0.2962 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1739 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 : 0.416 5.117 5730 Z= 0.228 Chirality : 0.036 0.130 682 Planarity : 0.002 0.022 680 Dihedral : 6.862 57.566 978 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % 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 are not related in a simple way. whole: 4.84 (0.36), residues: 512 helix: 3.59 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 1.33 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 47 TYR 0.012 0.001 TYR A 96 PHE 0.015 0.001 PHE A 109 TRP 0.006 0.001 TRP B 78 HIS 0.000 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 4192) covalent geometry : angle 0.41615 / 0.23 ( 5730) hydrogen bonds : bond 0.04240 / 2.86 ( 343) hydrogen bonds : angle 3.23880 / 2.46 ( 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 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.092 Fit side-chains REVERT: A 3 ARG cc_start: 0.6332 (ttt180) cc_final: 0.5951 (ttt-90) REVERT: A 47 ARG cc_start: 0.6438 (ttt-90) cc_final: 0.5994 (ttp80) REVERT: A 135 PHE cc_start: 0.7832 (t80) cc_final: 0.7553 (t80) REVERT: A 137 ARG cc_start: 0.6265 (ttm-80) cc_final: 0.5923 (ttp-170) REVERT: B 3 ARG cc_start: 0.6348 (ttt180) cc_final: 0.6027 (ttt-90) REVERT: B 47 ARG cc_start: 0.6433 (ttt-90) cc_final: 0.5993 (ttp80) REVERT: B 135 PHE cc_start: 0.7832 (t80) cc_final: 0.7551 (t80) REVERT: B 137 ARG cc_start: 0.6248 (ttm-80) cc_final: 0.5910 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.7451 time to fit residues: 47.3973 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 : 0.146 ------------------------------------------------------------------------------- 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: 0.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3631 r_free = 0.3631 target = 0.135494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102415 restraints weight = 4652.139| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.68 r_work: 0.3134 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4192 Z= 0.140 Angle : 0.432 5.138 5730 Z= 0.236 Chirality : 0.036 0.133 682 Planarity : 0.002 0.022 680 Dihedral : 6.890 58.744 978 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.26 % Allowed : 12.43 % Favored : 87.30 % 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 are not related in a simple way. whole: 4.77 (0.36), residues: 512 helix: 3.53 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 1.34 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 47 TYR 0.012 0.001 TYR A 96 PHE 0.015 0.001 PHE B 109 TRP 0.005 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4192) covalent geometry : angle 0.43220 / 0.24 ( 5730) hydrogen bonds : bond 0.04486 / 3.01 ( 343) hydrogen bonds : angle 3.28305 / 2.49 ( 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 63 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.151 Fit side-chains REVERT: A 3 ARG cc_start: 0.6550 (ttt180) cc_final: 0.6146 (ttt-90) REVERT: A 135 PHE cc_start: 0.7990 (t80) cc_final: 0.7702 (t80) REVERT: A 137 ARG cc_start: 0.6474 (ttm-80) cc_final: 0.6103 (ttp-170) REVERT: B 3 ARG cc_start: 0.6601 (ttt180) cc_final: 0.6266 (ttt-90) REVERT: B 135 PHE cc_start: 0.7998 (t80) cc_final: 0.7708 (t80) REVERT: B 137 ARG cc_start: 0.6476 (ttm-80) cc_final: 0.6105 (ttp-170) outliers start: 1 outliers final: 2 residues processed: 62 average time/residue: 0.7690 time to fit residues: 48.8998 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 : 0.145 ------------------------------------------------------------------------------- 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: 0.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3624 r_free = 0.3624 target = 0.135924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103311 restraints weight = 4592.857| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.67 r_work: 0.2979 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4192 Z= 0.115 Angle : 0.407 5.121 5730 Z= 0.222 Chirality : 0.035 0.128 682 Planarity : 0.002 0.021 680 Dihedral : 6.733 59.173 978 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.53 % Allowed : 12.17 % Favored : 87.30 % 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 are not related in a simple way. whole: 4.92 (0.36), residues: 512 helix: 3.67 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 1.22 (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 0.014 0.001 PHE A 109 TRP 0.005 0.001 TRP B 78 HIS 0.000 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 4192) covalent geometry : angle 0.40709 / 0.22 ( 5730) hydrogen bonds : bond 0.04042 / 2.73 ( 343) hydrogen bonds : angle 3.20333 / 2.43 ( 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 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.167 Fit side-chains REVERT: A 3 ARG cc_start: 0.6322 (ttt180) cc_final: 0.5934 (ttt-90) REVERT: A 135 PHE cc_start: 0.7799 (t80) cc_final: 0.7451 (t80) REVERT: A 137 ARG cc_start: 0.6180 (ttm-80) cc_final: 0.5835 (ttp-170) REVERT: B 3 ARG cc_start: 0.6365 (ttt180) cc_final: 0.6029 (ttt-90) REVERT: B 135 PHE cc_start: 0.7806 (t80) cc_final: 0.7460 (t80) REVERT: B 137 ARG cc_start: 0.6181 (ttm-80) cc_final: 0.5836 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.7554 time to fit residues: 48.0714 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3604 r_free = 0.3604 target = 0.134181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101478 restraints weight = 4707.082| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.67 r_work: 0.2955 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4192 Z= 0.139 Angle : 0.431 5.155 5730 Z= 0.235 Chirality : 0.036 0.133 682 Planarity : 0.002 0.022 680 Dihedral : 6.795 58.391 978 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % 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 are not related in a simple way. whole: 4.84 (0.36), residues: 512 helix: 3.59 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 1.32 (0.70), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 47 TYR 0.012 0.001 TYR A 96 PHE 0.015 0.001 PHE A 109 TRP 0.004 0.001 TRP A 78 HIS 0.000 0.000 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4192) covalent geometry : angle 0.43077 / 0.23 ( 5730) hydrogen bonds : bond 0.04426 / 2.97 ( 343) hydrogen bonds : angle 3.27256 / 2.48 ( 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 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.154 Fit side-chains REVERT: A 3 ARG cc_start: 0.6358 (ttt180) cc_final: 0.5965 (ttt-90) REVERT: A 135 PHE cc_start: 0.7837 (t80) cc_final: 0.7568 (t80) REVERT: A 137 ARG cc_start: 0.6278 (ttm-80) cc_final: 0.5928 (ttp-170) REVERT: B 3 ARG cc_start: 0.6398 (ttt180) cc_final: 0.6064 (ttt-90) REVERT: B 135 PHE cc_start: 0.7838 (t80) cc_final: 0.7567 (t80) REVERT: B 137 ARG cc_start: 0.6269 (ttm-80) cc_final: 0.5920 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.7664 time to fit residues: 48.6838 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 : 0.162 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.0010 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3626 r_free = 0.3626 target = 0.136049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103487 restraints weight = 4554.229| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.66 r_work: 0.2984 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1916 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= 0.114 Angle : 0.404 5.122 5730 Z= 0.221 Chirality : 0.035 0.126 682 Planarity : 0.002 0.021 680 Dihedral : 6.639 56.721 978 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % 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 are not related in a simple way. whole: 4.93 (0.36), residues: 512 helix: 3.67 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 1.24 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 47 TYR 0.011 0.001 TYR A 96 PHE 0.014 0.001 PHE B 109 TRP 0.005 0.001 TRP B 78 HIS 0.000 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 4192) covalent geometry : angle 0.40434 / 0.22 ( 5730) hydrogen bonds : bond 0.04022 / 2.71 ( 343) hydrogen bonds : angle 3.20251 / 2.43 ( 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 : 0.151 Fit side-chains REVERT: A 3 ARG cc_start: 0.6323 (ttt180) cc_final: 0.5937 (ttt-90) REVERT: A 135 PHE cc_start: 0.7824 (t80) cc_final: 0.7486 (t80) REVERT: A 137 ARG cc_start: 0.6195 (ttm-80) cc_final: 0.5847 (ttp-170) REVERT: B 3 ARG cc_start: 0.6363 (ttt180) cc_final: 0.6030 (ttt-90) REVERT: B 135 PHE cc_start: 0.7828 (t80) cc_final: 0.7490 (t80) REVERT: B 137 ARG cc_start: 0.6198 (ttm-80) cc_final: 0.5850 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.7949 time to fit residues: 50.4878 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 : 0.136 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3637 r_free = 0.3637 target = 0.136174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103371 restraints weight = 4579.990| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.67 r_work: 0.2963 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4192 Z= 0.130 Angle : 0.425 5.161 5730 Z= 0.231 Chirality : 0.036 0.129 682 Planarity : 0.002 0.021 680 Dihedral : 6.680 55.996 978 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % 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 are not related in a simple way. whole: 4.88 (0.36), residues: 512 helix: 3.62 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 1.33 (0.70), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.012 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/Z covalent geometry : bond 0.00288 / 0.13 ( 4192) covalent geometry : angle 0.42451 / 0.23 ( 5730) hydrogen bonds : bond 0.04291 / 2.88 ( 343) hydrogen bonds : angle 3.25062 / 2.47 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.57 seconds wall clock time: 33 minutes 6.52 seconds (1986.52 seconds total)