Starting phenix.real_space_refine on Tue Feb 3 14:12:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mek_48216/02_2026/9mek_48216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mek_48216/02_2026/9mek_48216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mek_48216/02_2026/9mek_48216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mek_48216/02_2026/9mek_48216.map" model { file = "/net/cci-nas-00/data/ceres_data/9mek_48216/02_2026/9mek_48216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mek_48216/02_2026/9mek_48216.cif" } resolution = 2.85 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= 0.062 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 4 8.98 5 S 12 5.16 5 C 2396 2.51 5 N 576 2.21 5 O 606 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: 3594 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1788 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1788 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 11 Unusual residues: {' K': 4, 'HP6': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'HP6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.17, per 1000 atoms: 0.33 Number of scatterers: 3594 At special positions: 0 Unit cell: (71.775, 61.625, 89.9, 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 4 19.00 S 12 16.00 O 606 8.00 N 576 7.00 C 2396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 53 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 109.3 milliseconds 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 892 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 77.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 7 through 51 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 72 through 78 removed outlier: 3.796A pdb=" N VAL A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 116 through 151 Proline residue: A 132 - end of helix removed outlier: 3.592A pdb=" N HIS A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 195 removed outlier: 3.608A pdb=" N TRP A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 230 through 264 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'B' and resid 8 through 51 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 55 through 69 Processing helix chain 'B' and resid 72 through 78 removed outlier: 3.796A pdb=" N VAL B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 116 through 151 Proline residue: B 132 - end of helix removed outlier: 3.592A pdb=" N HIS B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 213 Processing helix chain 'B' and resid 230 through 264 Processing helix chain 'B' and resid 267 through 271 280 hydrogen bonds defined for protein. 840 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: 0.33 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: 1.23 - 1.34: 1096 1.34 - 1.46: 832 1.46 - 1.58: 1726 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3670 Sorted by residual: bond pdb=" CA PRO A 226 " pdb=" C PRO A 226 " ideal model delta sigma weight residual 1.527 1.520 0.007 1.07e-02 8.73e+03 4.60e-01 bond pdb=" CA PRO B 226 " pdb=" C PRO B 226 " ideal model delta sigma weight residual 1.527 1.520 0.007 1.07e-02 8.73e+03 4.60e-01 bond pdb=" CA PRO B 226 " pdb=" CB PRO B 226 " ideal model delta sigma weight residual 1.530 1.537 -0.006 1.03e-02 9.43e+03 3.64e-01 bond pdb=" CA PRO A 226 " pdb=" CB PRO A 226 " ideal model delta sigma weight residual 1.530 1.537 -0.006 1.03e-02 9.43e+03 3.64e-01 bond pdb=" N PRO A 226 " pdb=" CA PRO A 226 " ideal model delta sigma weight residual 1.479 1.470 0.010 1.71e-02 3.42e+03 3.24e-01 ... (remaining 3665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 4780 1.01 - 2.02: 176 2.02 - 3.03: 44 3.03 - 4.05: 6 4.05 - 5.06: 14 Bond angle restraints: 5020 Sorted by residual: angle pdb=" N PHE A 185 " pdb=" CA PHE A 185 " pdb=" C PHE A 185 " ideal model delta sigma weight residual 114.75 110.69 4.06 1.26e+00 6.30e-01 1.04e+01 angle pdb=" N PHE B 185 " pdb=" CA PHE B 185 " pdb=" C PHE B 185 " ideal model delta sigma weight residual 114.75 110.69 4.06 1.26e+00 6.30e-01 1.04e+01 angle pdb=" CA PHE B 185 " pdb=" C PHE B 185 " pdb=" N LEU B 186 " ideal model delta sigma weight residual 119.80 117.04 2.76 1.34e+00 5.57e-01 4.25e+00 angle pdb=" CA PHE A 185 " pdb=" C PHE A 185 " pdb=" N LEU A 186 " ideal model delta sigma weight residual 119.80 117.04 2.76 1.34e+00 5.57e-01 4.25e+00 angle pdb=" N GLY B 130 " pdb=" CA GLY B 130 " pdb=" C GLY B 130 " ideal model delta sigma weight residual 113.18 117.61 -4.43 2.37e+00 1.78e-01 3.49e+00 ... (remaining 5015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.48: 1758 12.48 - 24.97: 221 24.97 - 37.45: 98 37.45 - 49.93: 26 49.93 - 62.41: 6 Dihedral angle restraints: 2109 sinusoidal: 727 harmonic: 1382 Sorted by residual: dihedral pdb=" CB ARG A 27 " pdb=" CG ARG A 27 " pdb=" CD ARG A 27 " pdb=" NE ARG A 27 " ideal model delta sinusoidal sigma weight residual -180.00 -127.27 -52.73 3 1.50e+01 4.44e-03 9.14e+00 dihedral pdb=" CB ARG B 27 " pdb=" CG ARG B 27 " pdb=" CD ARG B 27 " pdb=" NE ARG B 27 " ideal model delta sinusoidal sigma weight residual -180.00 -127.27 -52.73 3 1.50e+01 4.44e-03 9.14e+00 dihedral pdb=" N LEU A 43 " pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sinusoidal sigma weight residual -180.00 -129.61 -50.39 3 1.50e+01 4.44e-03 8.89e+00 ... (remaining 2106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 398 0.025 - 0.049: 146 0.049 - 0.073: 62 0.073 - 0.098: 14 0.098 - 0.122: 14 Chirality restraints: 634 Sorted by residual: chirality pdb=" CB THR A 42 " pdb=" CA THR A 42 " pdb=" OG1 THR A 42 " pdb=" CG2 THR A 42 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CB THR B 42 " pdb=" CA THR B 42 " pdb=" OG1 THR B 42 " pdb=" CG2 THR B 42 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA THR B 106 " pdb=" N THR B 106 " pdb=" C THR B 106 " pdb=" CB THR B 106 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 631 not shown) Planarity restraints: 606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 225 " -0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 226 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 226 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 226 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 225 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO B 226 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 226 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 226 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 181 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C VAL B 181 " 0.018 2.00e-02 2.50e+03 pdb=" O VAL B 181 " -0.007 2.00e-02 2.50e+03 pdb=" N THR B 182 " -0.006 2.00e-02 2.50e+03 ... (remaining 603 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.87: 1335 2.87 - 3.44: 4354 3.44 - 4.01: 6694 4.01 - 4.57: 9960 4.57 - 5.14: 13224 Nonbonded interactions: 35567 Sorted by model distance: nonbonded pdb=" O PHE A 209 " pdb=" OG SER A 213 " model vdw 2.306 3.040 nonbonded pdb=" O PHE B 209 " pdb=" OG SER B 213 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU A 29 " pdb=" N LEU B 115 " model vdw 2.311 3.120 nonbonded pdb=" N LEU A 115 " pdb=" OE2 GLU B 29 " model vdw 2.311 3.120 nonbonded pdb=" O SER B 101 " pdb=" OG1 THR B 105 " model vdw 2.318 3.040 ... (remaining 35562 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 7 through 271) selection = (chain 'B' and resid 7 through 271) } 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=0.28 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: 4.530 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.470 Find NCS groups from input model: 0.040 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3671 Z= 0.126 Angle : 0.526 5.058 5022 Z= 0.280 Chirality : 0.034 0.122 634 Planarity : 0.003 0.027 606 Dihedral : 14.272 62.411 1214 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.68 % Allowed : 20.11 % Favored : 78.21 % 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: 3.48 (0.40), residues: 466 helix: 2.94 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -1.00 (0.81), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 44 TYR 0.008 0.001 TYR B 206 PHE 0.009 0.002 PHE A 93 TRP 0.007 0.001 TRP A 199 HIS 0.006 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3670) covalent geometry : angle 0.52631 ( 5020) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.07131 ( 2) hydrogen bonds : bond 0.09847 ( 280) hydrogen bonds : angle 4.68874 ( 840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.079 Fit side-chains REVERT: A 11 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7605 (mm) REVERT: B 11 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7608 (mm) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 0.1747 time to fit residues: 6.7576 Evaluate side-chains 32 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 269 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.0170 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.190684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145787 restraints weight = 3382.749| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.76 r_work: 0.3596 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3671 Z= 0.131 Angle : 0.516 4.955 5022 Z= 0.258 Chirality : 0.035 0.137 634 Planarity : 0.004 0.029 606 Dihedral : 4.297 28.937 524 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 7.26 % Allowed : 16.76 % Favored : 75.98 % 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: 3.66 (0.40), residues: 466 helix: 3.02 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -0.62 (0.82), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 35 TYR 0.009 0.001 TYR B 220 PHE 0.011 0.002 PHE B 93 TRP 0.006 0.001 TRP B 199 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3670) covalent geometry : angle 0.51613 ( 5020) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.47639 ( 2) hydrogen bonds : bond 0.03324 ( 280) hydrogen bonds : angle 3.73403 ( 840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 32 time to evaluate : 0.126 Fit side-chains REVERT: A 11 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7733 (mm) REVERT: A 43 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6799 (mt) REVERT: A 112 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7327 (p) REVERT: B 11 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7760 (mm) REVERT: B 43 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6779 (mt) REVERT: B 112 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7330 (p) outliers start: 26 outliers final: 3 residues processed: 51 average time/residue: 0.2431 time to fit residues: 13.1805 Evaluate side-chains 40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 268 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.0040 chunk 17 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.187078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.141180 restraints weight = 3344.269| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.77 r_work: 0.3597 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3671 Z= 0.131 Angle : 0.502 5.199 5022 Z= 0.252 Chirality : 0.035 0.133 634 Planarity : 0.003 0.028 606 Dihedral : 4.097 30.871 520 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.91 % Allowed : 17.88 % Favored : 78.21 % 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: 3.66 (0.40), residues: 466 helix: 2.99 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -0.47 (0.86), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 35 TYR 0.009 0.001 TYR A 206 PHE 0.011 0.002 PHE A 93 TRP 0.007 0.001 TRP B 199 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3670) covalent geometry : angle 0.50168 ( 5020) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.20921 ( 2) hydrogen bonds : bond 0.03175 ( 280) hydrogen bonds : angle 3.52929 ( 840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.075 Fit side-chains REVERT: A 11 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7897 (mt) REVERT: A 43 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6667 (mp) REVERT: A 112 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7324 (p) REVERT: B 11 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7672 (mm) REVERT: B 112 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7310 (p) outliers start: 14 outliers final: 5 residues processed: 42 average time/residue: 0.2731 time to fit residues: 12.1456 Evaluate side-chains 40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.189024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142834 restraints weight = 3345.084| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.80 r_work: 0.3556 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3671 Z= 0.153 Angle : 0.517 5.558 5022 Z= 0.261 Chirality : 0.037 0.147 634 Planarity : 0.003 0.028 606 Dihedral : 4.285 31.110 520 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.47 % Allowed : 16.76 % Favored : 78.77 % 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: 3.52 (0.40), residues: 466 helix: 2.86 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.44 (0.86), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.010 0.002 TYR A 206 PHE 0.012 0.002 PHE B 93 TRP 0.008 0.001 TRP B 199 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3670) covalent geometry : angle 0.51721 ( 5020) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.02236 ( 2) hydrogen bonds : bond 0.03263 ( 280) hydrogen bonds : angle 3.54127 ( 840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 28 time to evaluate : 0.128 Fit side-chains REVERT: A 11 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7883 (mt) REVERT: B 11 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7670 (mm) outliers start: 16 outliers final: 6 residues processed: 40 average time/residue: 0.2365 time to fit residues: 10.2084 Evaluate side-chains 36 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 268 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.187049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139931 restraints weight = 3317.323| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.85 r_work: 0.3572 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3671 Z= 0.128 Angle : 0.510 5.342 5022 Z= 0.257 Chirality : 0.035 0.132 634 Planarity : 0.003 0.028 606 Dihedral : 4.159 31.578 520 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.35 % Allowed : 18.44 % Favored : 78.21 % 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: 3.63 (0.40), residues: 466 helix: 2.94 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.42 (0.86), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.010 0.002 TYR A 206 PHE 0.010 0.002 PHE A 122 TRP 0.007 0.001 TRP B 199 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3670) covalent geometry : angle 0.50965 ( 5020) SS BOND : bond 0.00021 ( 1) SS BOND : angle 0.00961 ( 2) hydrogen bonds : bond 0.03075 ( 280) hydrogen bonds : angle 3.42505 ( 840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.133 Fit side-chains REVERT: B 11 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7561 (mm) outliers start: 12 outliers final: 8 residues processed: 38 average time/residue: 0.2633 time to fit residues: 10.7705 Evaluate side-chains 37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.0370 chunk 23 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.189713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143295 restraints weight = 3322.971| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.81 r_work: 0.3567 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3671 Z= 0.131 Angle : 0.509 5.402 5022 Z= 0.256 Chirality : 0.035 0.132 634 Planarity : 0.003 0.028 606 Dihedral : 3.884 26.105 518 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.35 % Allowed : 18.16 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.66 (0.40), residues: 466 helix: 2.95 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.31 (0.87), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.010 0.002 TYR B 206 PHE 0.011 0.002 PHE B 93 TRP 0.008 0.001 TRP A 199 HIS 0.002 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3670) covalent geometry : angle 0.50932 ( 5020) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.08724 ( 2) hydrogen bonds : bond 0.03081 ( 280) hydrogen bonds : angle 3.39286 ( 840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.131 Fit side-chains REVERT: B 11 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7594 (mm) REVERT: B 43 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6562 (mp) outliers start: 12 outliers final: 7 residues processed: 40 average time/residue: 0.2245 time to fit residues: 9.6495 Evaluate side-chains 39 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 0.0170 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 0.0050 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.200632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155174 restraints weight = 3384.183| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.64 r_work: 0.3678 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3671 Z= 0.118 Angle : 0.513 5.291 5022 Z= 0.258 Chirality : 0.035 0.158 634 Planarity : 0.003 0.028 606 Dihedral : 3.790 26.305 518 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.79 % Allowed : 18.44 % Favored : 78.77 % 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: 3.74 (0.40), residues: 466 helix: 3.01 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.36 (0.86), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 37 TYR 0.010 0.002 TYR B 206 PHE 0.009 0.002 PHE B 122 TRP 0.007 0.001 TRP B 199 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3670) covalent geometry : angle 0.51329 ( 5020) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.02265 ( 2) hydrogen bonds : bond 0.02987 ( 280) hydrogen bonds : angle 3.33447 ( 840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.128 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 37 average time/residue: 0.2305 time to fit residues: 9.1638 Evaluate side-chains 32 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.0470 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.0370 chunk 42 optimal weight: 0.0570 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.201585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157944 restraints weight = 3305.505| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.79 r_work: 0.3701 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3671 Z= 0.104 Angle : 0.508 5.113 5022 Z= 0.251 Chirality : 0.035 0.152 634 Planarity : 0.003 0.028 606 Dihedral : 3.472 13.526 516 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.96 % Allowed : 18.72 % Favored : 79.33 % 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 (0.40), residues: 466 helix: 3.10 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.47 (0.84), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 37 TYR 0.010 0.001 TYR A 206 PHE 0.008 0.001 PHE B 122 TRP 0.006 0.001 TRP B 199 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 3670) covalent geometry : angle 0.50806 ( 5020) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.04524 ( 2) hydrogen bonds : bond 0.02847 ( 280) hydrogen bonds : angle 3.18223 ( 840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.131 Fit side-chains REVERT: B 11 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7867 (mm) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.2320 time to fit residues: 10.0405 Evaluate side-chains 35 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.199261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.155207 restraints weight = 3263.849| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.79 r_work: 0.3657 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3671 Z= 0.144 Angle : 0.540 5.534 5022 Z= 0.271 Chirality : 0.037 0.176 634 Planarity : 0.003 0.028 606 Dihedral : 3.703 13.818 516 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.96 % Allowed : 19.27 % Favored : 78.77 % 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: 3.65 (0.40), residues: 466 helix: 2.98 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.57 (0.83), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 37 TYR 0.011 0.002 TYR A 220 PHE 0.011 0.002 PHE B 93 TRP 0.008 0.001 TRP B 199 HIS 0.002 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3670) covalent geometry : angle 0.54039 ( 5020) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.09689 ( 2) hydrogen bonds : bond 0.03111 ( 280) hydrogen bonds : angle 3.32944 ( 840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.075 Fit side-chains REVERT: A 112 THR cc_start: 0.7941 (m) cc_final: 0.7731 (t) REVERT: B 11 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7969 (mm) REVERT: B 112 THR cc_start: 0.7941 (m) cc_final: 0.7737 (t) outliers start: 7 outliers final: 3 residues processed: 37 average time/residue: 0.1563 time to fit residues: 6.2375 Evaluate side-chains 34 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.0370 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.200049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156304 restraints weight = 3310.598| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.80 r_work: 0.3712 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3671 Z= 0.122 Angle : 0.525 5.331 5022 Z= 0.262 Chirality : 0.036 0.165 634 Planarity : 0.003 0.027 606 Dihedral : 3.601 13.153 516 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.12 % Allowed : 20.67 % Favored : 78.21 % 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: 3.73 (0.40), residues: 466 helix: 3.02 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.47 (0.84), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 35 TYR 0.011 0.002 TYR A 220 PHE 0.010 0.002 PHE A 122 TRP 0.007 0.001 TRP B 199 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3670) covalent geometry : angle 0.52490 ( 5020) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.07261 ( 2) hydrogen bonds : bond 0.02989 ( 280) hydrogen bonds : angle 3.27924 ( 840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.079 Fit side-chains REVERT: B 11 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7829 (mm) outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 0.2154 time to fit residues: 7.6256 Evaluate side-chains 32 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 0.0470 chunk 39 optimal weight: 0.9980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.199930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.156689 restraints weight = 3306.308| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.76 r_work: 0.3680 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3671 Z= 0.127 Angle : 0.505 5.489 5022 Z= 0.252 Chirality : 0.036 0.161 634 Planarity : 0.003 0.027 606 Dihedral : 3.640 13.218 516 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.40 % Allowed : 20.11 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.70 (0.40), residues: 466 helix: 2.99 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.39 (0.85), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 35 TYR 0.012 0.002 TYR B 220 PHE 0.010 0.002 PHE A 122 TRP 0.007 0.001 TRP B 199 HIS 0.002 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3670) covalent geometry : angle 0.50516 ( 5020) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.06253 ( 2) hydrogen bonds : bond 0.03042 ( 280) hydrogen bonds : angle 3.30817 ( 840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1376.99 seconds wall clock time: 24 minutes 14.32 seconds (1454.32 seconds total)