Starting phenix.real_space_refine on Tue Feb 3 14:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9w_51159/02_2026/9g9w_51159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9w_51159/02_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_51159/02_2026/9g9w_51159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9w_51159/02_2026/9g9w_51159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g9w_51159/02_2026/9g9w_51159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9w_51159/02_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-2.0-5952/lib/python3.9/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, 108 Unusual residues: {' K': 3, 'Y01': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 1.13, per 1000 atoms: 0.28 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: 0.33 Conformation dependent library (CDL) restraints added in 154.9 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: 0.10 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: 0.61 Time building geometry restraints manager: 0.45 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: 0.990 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: 5.690 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- 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 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 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 : 0.152 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: 0.5678 time to fit residues: 39.8077 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 : 0.151 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104335 restraints weight = 4610.317| |-----------------------------------------------------------------------------| 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: 0.2857 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 are 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 : 0.135 Fit side-chains REVERT: A 3 ARG cc_start: 0.6253 (ttt180) cc_final: 0.5966 (ttt-90) REVERT: A 135 PHE cc_start: 0.7860 (t80) cc_final: 0.7522 (t80) REVERT: A 137 ARG cc_start: 0.6321 (ttm-80) cc_final: 0.6019 (ttp-170) REVERT: B 3 ARG cc_start: 0.6256 (ttt180) cc_final: 0.5977 (ttt-90) REVERT: B 135 PHE cc_start: 0.7860 (t80) cc_final: 0.7522 (t80) REVERT: B 137 ARG cc_start: 0.6308 (ttm-80) cc_final: 0.6006 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.6929 time to fit residues: 44.0682 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 : 0.175 ------------------------------------------------------------------------------- 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: 0.0030 chunk 49 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 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: 2.9990 overall best weight: 0.9312 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.135127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101717 restraints weight = 4566.949| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.66 r_work: 0.2940 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4192 Z= 0.142 Angle : 0.438 5.033 5730 Z= 0.242 Chirality : 0.037 0.132 682 Planarity : 0.003 0.026 680 Dihedral : 7.174 52.894 978 Min Nonbonded Distance : 2.617 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 are not related in a simple way. whole: 4.27 (0.36), residues: 512 helix: 3.32 (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 0.013 0.002 TYR A 96 PHE 0.016 0.001 PHE A 109 TRP 0.010 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4192) covalent geometry : angle 0.43782 ( 5730) hydrogen bonds : bond 0.04695 ( 343) hydrogen bonds : angle 3.35143 ( 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 : 0.194 Fit side-chains REVERT: A 3 ARG cc_start: 0.6384 (ttt180) cc_final: 0.6043 (ttt-90) REVERT: A 51 LYS cc_start: 0.6693 (tttt) cc_final: 0.6452 (tttt) REVERT: A 135 PHE cc_start: 0.7880 (t80) cc_final: 0.7599 (t80) REVERT: A 137 ARG cc_start: 0.6367 (ttm-80) cc_final: 0.6022 (ttp-170) REVERT: B 3 ARG cc_start: 0.6364 (ttt180) cc_final: 0.5989 (ttt-90) REVERT: B 51 LYS cc_start: 0.6688 (tttt) cc_final: 0.6447 (tttt) REVERT: B 135 PHE cc_start: 0.7879 (t80) cc_final: 0.7596 (t80) REVERT: B 137 ARG cc_start: 0.6358 (ttm-80) cc_final: 0.6015 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 64 average time/residue: 0.7262 time to fit residues: 47.6592 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 : 0.144 ------------------------------------------------------------------------------- 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: 1.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.131469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098321 restraints weight = 4529.131| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.64 r_work: 0.2901 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4192 Z= 0.198 Angle : 0.487 5.118 5730 Z= 0.267 Chirality : 0.040 0.143 682 Planarity : 0.003 0.026 680 Dihedral : 7.264 52.979 978 Min Nonbonded Distance : 2.626 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 are not related in a simple way. whole: 4.32 (0.36), residues: 512 helix: 3.32 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.71 (0.70), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 236 TYR 0.014 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 72 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4192) covalent geometry : angle 0.48738 ( 5730) hydrogen bonds : bond 0.05370 ( 343) hydrogen bonds : angle 3.43808 ( 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: 0 poor density : 64 time to evaluate : 0.094 Fit side-chains REVERT: A 3 ARG cc_start: 0.6398 (ttt180) cc_final: 0.6065 (ttt-90) REVERT: A 51 LYS cc_start: 0.6693 (tttt) cc_final: 0.6440 (tttt) REVERT: A 135 PHE cc_start: 0.7842 (t80) cc_final: 0.7576 (t80) REVERT: A 137 ARG cc_start: 0.6314 (ttm-80) cc_final: 0.5968 (ttp-170) REVERT: B 3 ARG cc_start: 0.6430 (ttt180) cc_final: 0.6084 (ttt-90) REVERT: B 51 LYS cc_start: 0.6688 (tttt) cc_final: 0.6437 (tttt) REVERT: B 135 PHE cc_start: 0.7838 (t80) cc_final: 0.7572 (t80) REVERT: B 137 ARG cc_start: 0.6298 (ttm-80) cc_final: 0.5954 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 64 average time/residue: 0.7381 time to fit residues: 48.3597 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 : 0.149 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.136949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103665 restraints weight = 4486.869| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.65 r_work: 0.2965 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1695 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= 0.112 Angle : 0.398 5.047 5730 Z= 0.220 Chirality : 0.035 0.121 682 Planarity : 0.002 0.022 680 Dihedral : 6.933 55.376 978 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 4.70 (0.36), residues: 512 helix: 3.55 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 1.00 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 3 TYR 0.010 0.001 TYR A 96 PHE 0.015 0.001 PHE B 109 TRP 0.008 0.001 TRP B 78 HIS 0.000 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 4192) covalent geometry : angle 0.39845 ( 5730) hydrogen bonds : bond 0.04134 ( 343) hydrogen bonds : angle 3.18860 ( 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 : 0.158 Fit side-chains REVERT: A 3 ARG cc_start: 0.6359 (ttt180) cc_final: 0.6025 (ttt-90) REVERT: A 51 LYS cc_start: 0.6619 (tttt) cc_final: 0.6397 (tttt) REVERT: A 135 PHE cc_start: 0.7829 (t80) cc_final: 0.7485 (t80) REVERT: A 137 ARG cc_start: 0.6259 (ttm-80) cc_final: 0.5927 (ttp-170) REVERT: B 3 ARG cc_start: 0.6345 (ttt180) cc_final: 0.6011 (ttt-90) REVERT: B 51 LYS cc_start: 0.6615 (tttt) cc_final: 0.6394 (tttt) REVERT: B 135 PHE cc_start: 0.7830 (t80) cc_final: 0.7486 (t80) REVERT: B 137 ARG cc_start: 0.6243 (ttm-80) cc_final: 0.5915 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.8050 time to fit residues: 51.1414 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 : 0.144 ------------------------------------------------------------------------------- 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: 3.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.132448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099260 restraints weight = 4686.367| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.66 r_work: 0.2914 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1584 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= 0.174 Angle : 0.464 5.150 5730 Z= 0.254 Chirality : 0.038 0.138 682 Planarity : 0.002 0.023 680 Dihedral : 7.085 56.045 978 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 4.46 (0.36), residues: 512 helix: 3.42 (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 0.002 0.000 ARG A 47 TYR 0.012 0.002 TYR A 96 PHE 0.015 0.002 PHE B 109 TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 4192) covalent geometry : angle 0.46407 ( 5730) hydrogen bonds : bond 0.05010 ( 343) hydrogen bonds : angle 3.34809 ( 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 : 0.150 Fit side-chains REVERT: A 3 ARG cc_start: 0.6416 (ttt180) cc_final: 0.6034 (ttt-90) REVERT: A 51 LYS cc_start: 0.6758 (tttt) cc_final: 0.6522 (tttt) REVERT: A 135 PHE cc_start: 0.7841 (t80) cc_final: 0.7556 (t80) REVERT: A 137 ARG cc_start: 0.6292 (ttm-80) cc_final: 0.5934 (ttp-170) REVERT: B 3 ARG cc_start: 0.6420 (ttt180) cc_final: 0.6090 (ttt-90) REVERT: B 51 LYS cc_start: 0.6697 (tttt) cc_final: 0.6457 (tttt) REVERT: B 135 PHE cc_start: 0.7842 (t80) cc_final: 0.7557 (t80) REVERT: B 137 ARG cc_start: 0.6282 (ttm-80) cc_final: 0.5926 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.8038 time to fit residues: 51.0402 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 : 0.147 ------------------------------------------------------------------------------- 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: 0.9980 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.134612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101129 restraints weight = 4599.016| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.68 r_work: 0.2914 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1651 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= 0.149 Angle : 0.437 5.144 5730 Z= 0.240 Chirality : 0.037 0.132 682 Planarity : 0.002 0.022 680 Dihedral : 7.029 56.942 978 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 4.51 (0.36), residues: 512 helix: 3.43 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 0.85 (0.68), 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 0.005 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4192) covalent geometry : angle 0.43725 ( 5730) hydrogen bonds : bond 0.04698 ( 343) hydrogen bonds : angle 3.27803 ( 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 : 0.146 Fit side-chains REVERT: A 3 ARG cc_start: 0.6395 (ttt180) cc_final: 0.6012 (ttt-90) REVERT: A 47 ARG cc_start: 0.6423 (ttt-90) cc_final: 0.5980 (ttp80) REVERT: A 135 PHE cc_start: 0.7817 (t80) cc_final: 0.7553 (t80) REVERT: A 137 ARG cc_start: 0.6285 (ttm-80) cc_final: 0.5932 (ttp-170) REVERT: B 3 ARG cc_start: 0.6428 (ttt180) cc_final: 0.6096 (ttt-90) REVERT: B 47 ARG cc_start: 0.6412 (ttt-90) cc_final: 0.5973 (ttp80) REVERT: B 135 PHE cc_start: 0.7814 (t80) cc_final: 0.7549 (t80) REVERT: B 137 ARG cc_start: 0.6270 (ttm-80) cc_final: 0.5921 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.7571 time to fit residues: 48.0860 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 : 0.147 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 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: 0.2980 chunk 15 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.137938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104774 restraints weight = 4470.486| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.65 r_work: 0.2980 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1870 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= 0.105 Angle : 0.386 5.079 5730 Z= 0.212 Chirality : 0.034 0.119 682 Planarity : 0.002 0.021 680 Dihedral : 6.778 59.844 978 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 4.76 (0.36), residues: 512 helix: 3.63 (0.24), residues: 414 sheet: None (None), residues: 0 loop : 0.78 (0.65), 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 B 78 HIS 0.000 0.000 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 4192) covalent geometry : angle 0.38550 ( 5730) hydrogen bonds : bond 0.03887 ( 343) hydrogen bonds : angle 3.14227 ( 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 : 0.146 Fit side-chains REVERT: A 3 ARG cc_start: 0.6276 (ttt180) cc_final: 0.5901 (ttt-90) REVERT: A 135 PHE cc_start: 0.7794 (t80) cc_final: 0.7486 (t80) REVERT: A 137 ARG cc_start: 0.6205 (ttm-80) cc_final: 0.5865 (ttp-170) REVERT: B 3 ARG cc_start: 0.6325 (ttt180) cc_final: 0.6003 (ttt-90) REVERT: B 135 PHE cc_start: 0.7810 (t80) cc_final: 0.7504 (t80) REVERT: B 137 ARG cc_start: 0.6199 (ttm-80) cc_final: 0.5861 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 56 average time/residue: 0.7814 time to fit residues: 44.8799 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 : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=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: 0.9980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.135602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102303 restraints weight = 4592.345| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.67 r_work: 0.3071 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1799 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= 0.134 Angle : 0.422 5.159 5730 Z= 0.231 Chirality : 0.036 0.129 682 Planarity : 0.002 0.021 680 Dihedral : 6.828 59.114 978 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 4.69 (0.36), residues: 512 helix: 3.56 (0.24), residues: 414 sheet: None (None), residues: 0 loop : 0.87 (0.67), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4192) covalent geometry : angle 0.42199 ( 5730) hydrogen bonds : bond 0.04401 ( 343) hydrogen bonds : angle 3.22028 ( 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 : 0.178 Fit side-chains REVERT: A 3 ARG cc_start: 0.6318 (ttt180) cc_final: 0.5929 (ttt-90) REVERT: A 135 PHE cc_start: 0.7818 (t80) cc_final: 0.7492 (t80) REVERT: A 137 ARG cc_start: 0.6225 (ttm-80) cc_final: 0.5875 (ttp-170) REVERT: B 3 ARG cc_start: 0.6370 (ttt180) cc_final: 0.6039 (ttt-90) REVERT: B 135 PHE cc_start: 0.7819 (t80) cc_final: 0.7501 (t80) REVERT: B 137 ARG cc_start: 0.6228 (ttm-80) cc_final: 0.5877 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.8134 time to fit residues: 51.6621 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=1.00 ------------------------------------------------------------------------------- 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: 0.3980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 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: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.133640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100708 restraints weight = 4520.793| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.64 r_work: 0.2924 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1774 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= 0.146 Angle : 0.438 5.160 5730 Z= 0.239 Chirality : 0.037 0.130 682 Planarity : 0.002 0.021 680 Dihedral : 6.940 58.935 978 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 4.60 (0.36), residues: 512 helix: 3.50 (0.24), residues: 414 sheet: None (None), residues: 0 loop : 0.86 (0.67), 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 A 109 TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4192) covalent geometry : angle 0.43844 ( 5730) hydrogen bonds : bond 0.04602 ( 343) hydrogen bonds : angle 3.25699 ( 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 : 0.092 Fit side-chains REVERT: A 3 ARG cc_start: 0.6377 (ttt180) cc_final: 0.5991 (ttt-90) REVERT: A 135 PHE cc_start: 0.7841 (t80) cc_final: 0.7574 (t80) REVERT: A 137 ARG cc_start: 0.6278 (ttm-80) cc_final: 0.5922 (ttp-170) REVERT: B 3 ARG cc_start: 0.6414 (ttt180) cc_final: 0.6084 (ttt-90) REVERT: B 135 PHE cc_start: 0.7835 (t80) cc_final: 0.7567 (t80) REVERT: B 137 ARG cc_start: 0.6272 (ttm-80) cc_final: 0.5918 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 0.7764 time to fit residues: 49.2805 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 : 0.144 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 0.0020 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: 2.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.137222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103960 restraints weight = 4502.228| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.66 r_work: 0.2970 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1918 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= 0.113 Angle : 0.403 5.118 5730 Z= 0.219 Chirality : 0.035 0.121 682 Planarity : 0.002 0.021 680 Dihedral : 6.721 57.194 978 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.61 (0.24), residues: 414 sheet: None (None), residues: 0 loop : 0.86 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.010 0.001 TYR B 96 PHE 0.014 0.001 PHE B 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 0.00238 ( 4192) covalent geometry : angle 0.40269 ( 5730) hydrogen bonds : bond 0.04027 ( 343) hydrogen bonds : angle 3.16958 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2004.85 seconds wall clock time: 34 minutes 46.53 seconds (2086.53 seconds total)