Starting phenix.real_space_refine on Fri Aug 22 15:05:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bws_44978/08_2025/9bws_44978_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bws_44978/08_2025/9bws_44978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bws_44978/08_2025/9bws_44978_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bws_44978/08_2025/9bws_44978_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bws_44978/08_2025/9bws_44978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bws_44978/08_2025/9bws_44978.map" } resolution = 2.39 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= 0.014 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 28 5.16 5 C 2868 2.51 5 N 678 2.21 5 O 708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4286 Number of models: 1 Model: "" Number of chains: 4 Chain: "U" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2051 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Chain: "A" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2051 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Chain: "U" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 91 Unusual residues: {' K': 1, 'D10': 2, 'D12': 1, 'EIC': 1, 'HEX': 1, 'OCT': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 93 Unusual residues: {' K': 3, 'D10': 2, 'D12': 1, 'EIC': 1, 'HEX': 1, 'OCT': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 1.04, per 1000 atoms: 0.24 Number of scatterers: 4286 At special positions: 0 Unit cell: (68.47, 74.315, 94.355, 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 28 16.00 O 708 8.00 N 678 7.00 C 2868 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 183.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'U' and resid 14 through 65 removed outlier: 5.540A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS U 45 " --> pdb=" O LEU U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 83 Processing helix chain 'U' and resid 97 through 109 Processing helix chain 'U' and resid 124 through 162 Proline residue: U 136 - end of helix Processing helix chain 'U' and resid 193 through 215 removed outlier: 3.912A pdb=" N MET U 215 " --> pdb=" O CYS U 211 " (cutoff:3.500A) Processing helix chain 'U' and resid 223 through 236 Processing helix chain 'U' and resid 255 through 294 removed outlier: 3.759A pdb=" N PHE U 259 " --> pdb=" O GLY U 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 64 removed outlier: 5.555A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 85 removed outlier: 3.589A pdb=" N GLU A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 122 through 162 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 193 through 220 removed outlier: 3.582A pdb=" N MET A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 255 through 294 removed outlier: 3.869A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 984 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: 0.56 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 723 1.33 - 1.45: 1183 1.45 - 1.57: 2422 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4368 Sorted by residual: bond pdb=" N ILE A 86 " pdb=" CA ILE A 86 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.63e+00 bond pdb=" N TYR U 216 " pdb=" CA TYR U 216 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.55e+00 bond pdb=" N SER A 67 " pdb=" CA SER A 67 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.18e-02 7.18e+03 7.30e+00 bond pdb=" CA ALA A 84 " pdb=" CB ALA A 84 " ideal model delta sigma weight residual 1.529 1.482 0.047 1.74e-02 3.30e+03 7.20e+00 bond pdb=" N GLU A 79 " pdb=" CA GLU A 79 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.46e+00 ... (remaining 4363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 5559 1.39 - 2.78: 206 2.78 - 4.17: 54 4.17 - 5.56: 18 5.56 - 6.95: 3 Bond angle restraints: 5840 Sorted by residual: angle pdb=" N ALA A 84 " pdb=" CA ALA A 84 " pdb=" C ALA A 84 " ideal model delta sigma weight residual 112.54 107.85 4.69 1.22e+00 6.72e-01 1.48e+01 angle pdb=" N GLU A 80 " pdb=" CA GLU A 80 " pdb=" CB GLU A 80 " ideal model delta sigma weight residual 110.22 104.77 5.45 1.54e+00 4.22e-01 1.25e+01 angle pdb=" CA TYR U 216 " pdb=" CB TYR U 216 " pdb=" CG TYR U 216 " ideal model delta sigma weight residual 113.90 119.91 -6.01 1.80e+00 3.09e-01 1.11e+01 angle pdb=" N GLU U 220 " pdb=" CA GLU U 220 " pdb=" C GLU U 220 " ideal model delta sigma weight residual 109.54 114.03 -4.49 1.37e+00 5.33e-01 1.07e+01 angle pdb=" N GLY U 221 " pdb=" CA GLY U 221 " pdb=" C GLY U 221 " ideal model delta sigma weight residual 113.18 120.13 -6.95 2.37e+00 1.78e-01 8.61e+00 ... (remaining 5835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 2234 17.78 - 35.56: 240 35.56 - 53.34: 47 53.34 - 71.12: 12 71.12 - 88.91: 1 Dihedral angle restraints: 2534 sinusoidal: 1048 harmonic: 1486 Sorted by residual: dihedral pdb=" CA ASP U 96 " pdb=" C ASP U 96 " pdb=" N PHE U 97 " pdb=" CA PHE U 97 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ASP A 89 " pdb=" C ASP A 89 " pdb=" N ASN A 90 " pdb=" CA ASN A 90 " ideal model delta harmonic sigma weight residual 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TRP A 95 " pdb=" C TRP A 95 " pdb=" N ASP A 96 " pdb=" CA ASP A 96 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 2531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 444 0.030 - 0.059: 119 0.059 - 0.089: 47 0.089 - 0.119: 20 0.119 - 0.148: 4 Chirality restraints: 634 Sorted by residual: chirality pdb=" CA TYR U 216 " pdb=" N TYR U 216 " pdb=" C TYR U 216 " pdb=" CB TYR U 216 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE A 86 " pdb=" N ILE A 86 " pdb=" C ILE A 86 " pdb=" CB ILE A 86 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ALA A 84 " pdb=" N ALA A 84 " pdb=" C ALA A 84 " pdb=" CB ALA A 84 " both_signs ideal model delta sigma weight residual False 2.48 2.62 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 631 not shown) Planarity restraints: 712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 83 " -0.283 9.50e-02 1.11e+02 1.27e-01 9.89e+00 pdb=" NE ARG A 83 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 83 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 83 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 83 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 210 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C CYS A 210 " -0.042 2.00e-02 2.50e+03 pdb=" O CYS A 210 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS A 211 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 292 " 0.177 9.50e-02 1.11e+02 7.99e-02 5.22e+00 pdb=" NE ARG U 292 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG U 292 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG U 292 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG U 292 " -0.000 2.00e-02 2.50e+03 ... (remaining 709 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 1490 2.86 - 3.43: 4608 3.43 - 4.00: 7451 4.00 - 4.57: 10948 4.57 - 5.14: 15350 Nonbonded interactions: 39847 Sorted by model distance: nonbonded pdb=" O GLU A 79 " pdb=" OG1 THR A 82 " model vdw 2.288 3.040 nonbonded pdb=" O SER A 236 " pdb=" OG1 THR A 237 " model vdw 2.345 3.040 nonbonded pdb=" O SER U 236 " pdb=" OG1 THR U 237 " model vdw 2.385 3.040 nonbonded pdb=" N ASP U 96 " pdb=" OD1 ASP U 96 " model vdw 2.402 3.120 nonbonded pdb=" OE1 GLU U 46 " pdb=" O ARG A 94 " model vdw 2.411 3.040 ... (remaining 39842 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 14 through 295 or resid 404 or resid 410)) selection = (chain 'U' and (resid 14 through 295 or resid 404 or resid 410)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 5.230 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:5.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.004 0.047 4368 Z= 0.250 Angle : 0.677 6.953 5840 Z= 0.376 Chirality : 0.036 0.148 634 Planarity : 0.008 0.127 712 Dihedral : 14.795 88.905 1582 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.93 % Allowed : 11.34 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.00 (0.39), residues: 506 helix: 3.87 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -2.17 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG U 292 TYR 0.009 0.001 TYR U 216 PHE 0.010 0.002 PHE A 232 TRP 0.017 0.002 TRP U 53 HIS 0.004 0.001 HIS U 77 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 4368) covalent geometry : angle 0.67652 ( 5840) hydrogen bonds : bond 0.10917 ( 328) hydrogen bonds : angle 3.69557 ( 984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.169 Fit side-chains REVERT: U 251 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.6626 (t80) REVERT: A 251 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.6083 (t80) outliers start: 4 outliers final: 2 residues processed: 113 average time/residue: 0.6367 time to fit residues: 73.8704 Evaluate side-chains 80 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.0370 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 48 GLN A 48 GLN A 65 GLN A 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079537 restraints weight = 7419.451| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.45 r_work: 0.2854 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4368 Z= 0.127 Angle : 0.520 5.210 5840 Z= 0.282 Chirality : 0.034 0.182 634 Planarity : 0.003 0.023 712 Dihedral : 9.510 59.472 691 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.08 % Allowed : 15.51 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.61 (0.38), residues: 506 helix: 3.81 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.68 (0.70), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 292 TYR 0.017 0.001 TYR U 195 PHE 0.009 0.001 PHE U 232 TRP 0.011 0.001 TRP U 95 HIS 0.003 0.001 HIS U 64 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4368) covalent geometry : angle 0.52044 ( 5840) hydrogen bonds : bond 0.04729 ( 328) hydrogen bonds : angle 2.87294 ( 984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.165 Fit side-chains REVERT: U 54 GLU cc_start: 0.8761 (tp30) cc_final: 0.8287 (tp30) REVERT: U 62 ARG cc_start: 0.8532 (ttp-110) cc_final: 0.8144 (ttp-110) REVERT: U 220 GLU cc_start: 0.8245 (pt0) cc_final: 0.7817 (pt0) REVERT: U 251 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 62 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.8248 (ttp-110) REVERT: A 191 LYS cc_start: 0.8909 (pmmt) cc_final: 0.8494 (mppt) REVERT: A 251 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.6488 (t80) outliers start: 9 outliers final: 2 residues processed: 94 average time/residue: 0.6780 time to fit residues: 65.3878 Evaluate side-chains 85 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.080124 restraints weight = 7340.779| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.41 r_work: 0.2866 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4368 Z= 0.114 Angle : 0.502 7.019 5840 Z= 0.263 Chirality : 0.033 0.184 634 Planarity : 0.003 0.026 712 Dihedral : 8.041 56.806 688 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.85 % Allowed : 16.20 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.85 (0.38), residues: 506 helix: 3.96 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.49 (0.73), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 87 TYR 0.007 0.001 TYR A 195 PHE 0.005 0.001 PHE A 232 TRP 0.012 0.001 TRP U 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4368) covalent geometry : angle 0.50171 ( 5840) hydrogen bonds : bond 0.04272 ( 328) hydrogen bonds : angle 2.70377 ( 984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.099 Fit side-chains REVERT: U 54 GLU cc_start: 0.8752 (tp30) cc_final: 0.8449 (tp30) REVERT: U 220 GLU cc_start: 0.8184 (pt0) cc_final: 0.7878 (pt0) REVERT: U 251 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.6795 (t80) REVERT: A 251 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.8104 (m-80) outliers start: 8 outliers final: 3 residues processed: 85 average time/residue: 0.7064 time to fit residues: 61.5100 Evaluate side-chains 82 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 36 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.097625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.075299 restraints weight = 7302.502| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.42 r_work: 0.2800 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4368 Z= 0.130 Angle : 0.552 7.719 5840 Z= 0.294 Chirality : 0.033 0.187 634 Planarity : 0.003 0.022 712 Dihedral : 7.943 59.910 688 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.62 % Allowed : 15.28 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.85 (0.38), residues: 506 helix: 3.96 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.53 (0.73), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 292 TYR 0.014 0.001 TYR U 195 PHE 0.009 0.001 PHE A 97 TRP 0.008 0.001 TRP U 53 HIS 0.004 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4368) covalent geometry : angle 0.55242 ( 5840) hydrogen bonds : bond 0.04669 ( 328) hydrogen bonds : angle 2.75981 ( 984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.142 Fit side-chains REVERT: U 54 GLU cc_start: 0.8788 (tp30) cc_final: 0.8416 (tp30) REVERT: U 251 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.6937 (t80) REVERT: U 292 ARG cc_start: 0.8975 (ttm-80) cc_final: 0.8623 (ttm110) REVERT: A 51 GLN cc_start: 0.8806 (tp40) cc_final: 0.8553 (tm-30) REVERT: A 54 GLU cc_start: 0.8739 (tp30) cc_final: 0.8505 (tp30) REVERT: A 251 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.6238 (t80) REVERT: A 292 ARG cc_start: 0.8926 (ttm-80) cc_final: 0.8638 (ttm110) outliers start: 7 outliers final: 1 residues processed: 78 average time/residue: 0.7347 time to fit residues: 58.7023 Evaluate side-chains 68 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.0000 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.098512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.076393 restraints weight = 7202.740| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.39 r_work: 0.2788 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4368 Z= 0.128 Angle : 0.525 5.390 5840 Z= 0.279 Chirality : 0.033 0.193 634 Planarity : 0.003 0.023 712 Dihedral : 7.803 58.878 688 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.39 % Allowed : 14.58 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.84 (0.38), residues: 506 helix: 3.99 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.71 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 292 TYR 0.014 0.001 TYR U 195 PHE 0.007 0.001 PHE A 97 TRP 0.007 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4368) covalent geometry : angle 0.52508 ( 5840) hydrogen bonds : bond 0.04637 ( 328) hydrogen bonds : angle 2.76521 ( 984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.102 Fit side-chains REVERT: U 51 GLN cc_start: 0.8793 (tp40) cc_final: 0.8495 (tm-30) REVERT: U 54 GLU cc_start: 0.8792 (tp30) cc_final: 0.8272 (tp30) REVERT: U 251 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.6904 (t80) REVERT: U 292 ARG cc_start: 0.8939 (ttm-80) cc_final: 0.8603 (ttm110) REVERT: A 51 GLN cc_start: 0.8789 (tp40) cc_final: 0.8520 (tm-30) REVERT: A 54 GLU cc_start: 0.8728 (tp30) cc_final: 0.8483 (tp30) REVERT: A 292 ARG cc_start: 0.8897 (ttm-80) cc_final: 0.8605 (ttm110) outliers start: 6 outliers final: 3 residues processed: 74 average time/residue: 0.7278 time to fit residues: 55.1056 Evaluate side-chains 75 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.096087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.073766 restraints weight = 7337.663| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.41 r_work: 0.2747 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4368 Z= 0.142 Angle : 0.549 5.594 5840 Z= 0.293 Chirality : 0.034 0.189 634 Planarity : 0.003 0.022 712 Dihedral : 7.786 58.638 686 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.16 % Allowed : 15.97 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.76 (0.38), residues: 506 helix: 3.95 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.80 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U 292 TYR 0.013 0.001 TYR U 195 PHE 0.009 0.001 PHE A 97 TRP 0.007 0.001 TRP U 53 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4368) covalent geometry : angle 0.54927 ( 5840) hydrogen bonds : bond 0.05008 ( 328) hydrogen bonds : angle 2.83546 ( 984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.167 Fit side-chains REVERT: U 51 GLN cc_start: 0.8819 (tp40) cc_final: 0.8515 (tm-30) REVERT: U 54 GLU cc_start: 0.8788 (tp30) cc_final: 0.8441 (tp30) REVERT: U 190 TRP cc_start: 0.8028 (m100) cc_final: 0.7732 (m-10) REVERT: U 196 TYR cc_start: 0.8016 (m-10) cc_final: 0.7802 (m-80) REVERT: U 251 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.6960 (t80) REVERT: U 292 ARG cc_start: 0.8938 (ttm-80) cc_final: 0.8611 (ttm110) REVERT: A 51 GLN cc_start: 0.8780 (tp40) cc_final: 0.8500 (tm-30) REVERT: A 54 GLU cc_start: 0.8717 (tp30) cc_final: 0.8470 (tp30) REVERT: A 292 ARG cc_start: 0.8956 (ttm-80) cc_final: 0.8641 (ttm110) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.7150 time to fit residues: 52.8306 Evaluate side-chains 74 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.074316 restraints weight = 7284.556| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.42 r_work: 0.2754 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4368 Z= 0.137 Angle : 0.552 6.234 5840 Z= 0.294 Chirality : 0.034 0.189 634 Planarity : 0.003 0.022 712 Dihedral : 7.708 56.702 686 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.93 % Allowed : 16.67 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.77 (0.38), residues: 506 helix: 3.95 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.80 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 62 TYR 0.013 0.001 TYR U 195 PHE 0.007 0.001 PHE A 97 TRP 0.006 0.001 TRP U 53 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4368) covalent geometry : angle 0.55203 ( 5840) hydrogen bonds : bond 0.04851 ( 328) hydrogen bonds : angle 2.80154 ( 984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.123 Fit side-chains REVERT: U 51 GLN cc_start: 0.8806 (tp40) cc_final: 0.8503 (tm-30) REVERT: U 54 GLU cc_start: 0.8778 (tp30) cc_final: 0.8437 (tp30) REVERT: U 190 TRP cc_start: 0.8057 (m100) cc_final: 0.7741 (m-10) REVERT: U 251 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.6962 (t80) REVERT: U 292 ARG cc_start: 0.8954 (ttm-80) cc_final: 0.8607 (ttm110) REVERT: A 51 GLN cc_start: 0.8760 (tp40) cc_final: 0.8471 (tm-30) REVERT: A 54 GLU cc_start: 0.8687 (tp30) cc_final: 0.8398 (tp30) REVERT: A 292 ARG cc_start: 0.8922 (ttm-80) cc_final: 0.8603 (ttm110) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.6344 time to fit residues: 48.8310 Evaluate side-chains 78 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 156 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.095864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.073513 restraints weight = 7214.540| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.41 r_work: 0.2743 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4368 Z= 0.146 Angle : 0.579 7.185 5840 Z= 0.308 Chirality : 0.034 0.192 634 Planarity : 0.003 0.022 712 Dihedral : 7.686 54.611 686 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.93 % Allowed : 17.36 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.76 (0.38), residues: 506 helix: 3.95 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.81 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.012 0.001 TYR U 195 PHE 0.010 0.001 PHE A 97 TRP 0.006 0.001 TRP U 53 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4368) covalent geometry : angle 0.57868 ( 5840) hydrogen bonds : bond 0.05003 ( 328) hydrogen bonds : angle 2.83203 ( 984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.120 Fit side-chains REVERT: U 51 GLN cc_start: 0.8822 (tp40) cc_final: 0.8510 (tm-30) REVERT: U 54 GLU cc_start: 0.8786 (tp30) cc_final: 0.8465 (tp30) REVERT: U 190 TRP cc_start: 0.8088 (m100) cc_final: 0.7799 (m-10) REVERT: U 251 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.6971 (t80) REVERT: U 292 ARG cc_start: 0.8948 (ttm-80) cc_final: 0.8624 (ttm110) REVERT: A 51 GLN cc_start: 0.8800 (tp40) cc_final: 0.8506 (tm-30) REVERT: A 54 GLU cc_start: 0.8665 (tp30) cc_final: 0.8386 (tp30) REVERT: A 292 ARG cc_start: 0.8941 (ttm-80) cc_final: 0.8624 (ttm110) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.7295 time to fit residues: 56.0528 Evaluate side-chains 76 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 156 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.096228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.073803 restraints weight = 7277.121| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.43 r_work: 0.2745 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4368 Z= 0.144 Angle : 0.590 7.846 5840 Z= 0.314 Chirality : 0.034 0.195 634 Planarity : 0.003 0.023 712 Dihedral : 7.454 51.626 686 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.93 % Allowed : 17.59 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.77 (0.38), residues: 506 helix: 3.96 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.79 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.011 0.001 TYR A 195 PHE 0.008 0.001 PHE A 97 TRP 0.007 0.001 TRP U 53 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4368) covalent geometry : angle 0.58985 ( 5840) hydrogen bonds : bond 0.04919 ( 328) hydrogen bonds : angle 2.81634 ( 984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.155 Fit side-chains REVERT: U 51 GLN cc_start: 0.8825 (tp40) cc_final: 0.8515 (tm-30) REVERT: U 54 GLU cc_start: 0.8786 (tp30) cc_final: 0.8452 (tp30) REVERT: U 190 TRP cc_start: 0.8101 (m100) cc_final: 0.7817 (m-10) REVERT: U 251 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.6940 (t80) REVERT: U 292 ARG cc_start: 0.8943 (ttm-80) cc_final: 0.8609 (ttm110) REVERT: A 51 GLN cc_start: 0.8797 (tp40) cc_final: 0.8499 (tm-30) REVERT: A 54 GLU cc_start: 0.8647 (tp30) cc_final: 0.8367 (tp30) REVERT: A 292 ARG cc_start: 0.8934 (ttm-80) cc_final: 0.8621 (ttm110) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.7278 time to fit residues: 55.2266 Evaluate side-chains 76 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.0070 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.074002 restraints weight = 7237.094| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.43 r_work: 0.2749 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4368 Z= 0.145 Angle : 0.607 8.401 5840 Z= 0.323 Chirality : 0.034 0.200 634 Planarity : 0.003 0.024 712 Dihedral : 7.305 49.667 686 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.69 % Allowed : 17.59 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.78 (0.38), residues: 506 helix: 3.97 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.82 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.011 0.001 TYR A 195 PHE 0.010 0.001 PHE A 97 TRP 0.007 0.001 TRP U 95 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4368) covalent geometry : angle 0.60737 ( 5840) hydrogen bonds : bond 0.04860 ( 328) hydrogen bonds : angle 2.79803 ( 984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.121 Fit side-chains REVERT: U 51 GLN cc_start: 0.8823 (tp40) cc_final: 0.8505 (tm-30) REVERT: U 54 GLU cc_start: 0.8765 (tp30) cc_final: 0.8324 (tp30) REVERT: U 190 TRP cc_start: 0.8082 (m100) cc_final: 0.7787 (m-10) REVERT: U 251 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.6941 (t80) REVERT: U 292 ARG cc_start: 0.8929 (ttm-80) cc_final: 0.8595 (ttm110) REVERT: A 51 GLN cc_start: 0.8787 (tp40) cc_final: 0.8480 (tm-30) REVERT: A 54 GLU cc_start: 0.8639 (tp30) cc_final: 0.8265 (tp30) REVERT: A 292 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8620 (ttm110) outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.7308 time to fit residues: 54.7001 Evaluate side-chains 74 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.074269 restraints weight = 7174.829| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.42 r_work: 0.2755 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4368 Z= 0.144 Angle : 0.600 8.506 5840 Z= 0.320 Chirality : 0.034 0.197 634 Planarity : 0.003 0.024 712 Dihedral : 7.210 49.200 686 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.69 % Allowed : 17.59 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.81 (0.38), residues: 506 helix: 3.98 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.78 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.007 0.001 TYR U 78 PHE 0.007 0.001 PHE A 97 TRP 0.007 0.001 TRP U 53 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4368) covalent geometry : angle 0.60037 ( 5840) hydrogen bonds : bond 0.04819 ( 328) hydrogen bonds : angle 2.79563 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.90 seconds wall clock time: 33 minutes 16.68 seconds (1996.68 seconds total)