Starting phenix.real_space_refine on Thu Jul 2 00:22:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bws_44978/07_2026/9bws_44978_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bws_44978/07_2026/9bws_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_44978/07_2026/9bws_44978_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bws_44978/07_2026/9bws_44978_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bws_44978/07_2026/9bws_44978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bws_44978/07_2026/9bws_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-dev-6108/lib/python3.11/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, 90 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'D10': 2, 'D12': 1, 'EIC': 1, 'HEX': 1, 'OCT': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 90 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'D10': 2, 'D12': 1, 'EIC': 1, 'HEX': 1, 'OCT': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 3 Time building chain proxies: 1.34, per 1000 atoms: 0.31 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: 0.62 Conformation dependent library (CDL) restraints added in 170.4 milliseconds 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: 0.08 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: 0.51 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.000 Process input model: 6.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 are 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/Z covalent geometry : bond 0.00391 / 0.25 ( 4368) covalent geometry : angle 0.67652 / 0.38 ( 5840) hydrogen bonds : bond 0.10917 / 7.18 ( 328) hydrogen bonds : angle 3.69557 / 2.79 ( 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 : 0.160 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: 0.6564 time to fit residues: 76.2230 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 : 0.101 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3353 r_free = 0.3353 target = 0.100949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.079295 restraints weight = 7416.095| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.46 r_work: 0.2872 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4368 Z= 0.131 Angle : 0.530 5.139 5840 Z= 0.287 Chirality : 0.034 0.165 634 Planarity : 0.003 0.028 712 Dihedral : 9.834 59.672 691 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.08 % Allowed : 15.74 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.58 (0.38), residues: 506 helix: 3.84 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.93 (0.68), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG U 148 TYR 0.016 0.001 TYR U 195 PHE 0.009 0.001 PHE U 232 TRP 0.011 0.001 TRP U 95 HIS 0.004 0.001 HIS U 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 4368) covalent geometry : angle 0.53002 / 0.29 ( 5840) hydrogen bonds : bond 0.04930 / 3.36 ( 328) hydrogen bonds : angle 2.92153 / 2.26 ( 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 97 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.169 Fit side-chains REVERT: U 54 GLU cc_start: 0.8776 (tp30) cc_final: 0.8532 (tp30) REVERT: U 251 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.6987 (t80) REVERT: A 62 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8226 (ttp-110) REVERT: A 251 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.6533 (t80) outliers start: 9 outliers final: 2 residues processed: 93 average time/residue: 0.7436 time to fit residues: 70.9671 Evaluate side-chains 82 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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: 0.0060 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.076504 restraints weight = 7386.827| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.43 r_work: 0.2814 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4368 Z= 0.126 Angle : 0.527 6.878 5840 Z= 0.278 Chirality : 0.033 0.185 634 Planarity : 0.003 0.030 712 Dihedral : 8.395 56.053 688 Min Nonbonded Distance : 2.487 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 are not related in a simple way. whole: 4.75 (0.38), residues: 506 helix: 3.91 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.64 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 292 TYR 0.008 0.001 TYR U 78 PHE 0.007 0.001 PHE A 232 TRP 0.012 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 4368) covalent geometry : angle 0.52672 / 0.28 ( 5840) hydrogen bonds : bond 0.04676 / 3.20 ( 328) hydrogen bonds : angle 2.81360 / 2.19 ( 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 85 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.164 Fit side-chains REVERT: U 54 GLU cc_start: 0.8786 (tp30) cc_final: 0.8494 (tp30) REVERT: U 251 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.6928 (t80) REVERT: A 51 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8501 (tp40) REVERT: A 54 GLU cc_start: 0.8754 (tp30) cc_final: 0.8541 (tp30) REVERT: A 251 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: A 292 ARG cc_start: 0.8910 (ttm-80) cc_final: 0.8657 (ttm110) outliers start: 8 outliers final: 1 residues processed: 80 average time/residue: 0.8317 time to fit residues: 68.1180 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 : 0.100 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.096881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.074553 restraints weight = 7306.137| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.41 r_work: 0.2780 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4368 Z= 0.133 Angle : 0.533 5.428 5840 Z= 0.283 Chirality : 0.033 0.184 634 Planarity : 0.003 0.023 712 Dihedral : 8.323 59.860 688 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.16 % Allowed : 15.74 % 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 are not related in a simple way. whole: 4.76 (0.38), residues: 506 helix: 3.90 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.58 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 292 TYR 0.013 0.001 TYR U 195 PHE 0.008 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/Z covalent geometry : bond 0.00291 / 0.13 ( 4368) covalent geometry : angle 0.53253 / 0.28 ( 5840) hydrogen bonds : bond 0.04860 / 3.33 ( 328) hydrogen bonds : angle 2.85527 / 2.22 ( 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 79 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.158 Fit side-chains REVERT: U 51 GLN cc_start: 0.8803 (tp40) cc_final: 0.8549 (tm-30) REVERT: U 54 GLU cc_start: 0.8784 (tp30) cc_final: 0.8501 (tp30) REVERT: U 251 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.6965 (t80) REVERT: U 292 ARG cc_start: 0.8972 (ttm-80) cc_final: 0.8644 (ttm110) REVERT: A 51 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8543 (tm-30) REVERT: A 54 GLU cc_start: 0.8742 (tp30) cc_final: 0.8467 (tp30) REVERT: A 251 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: A 292 ARG cc_start: 0.8916 (ttm-80) cc_final: 0.8644 (ttm110) outliers start: 5 outliers final: 2 residues processed: 76 average time/residue: 0.8344 time to fit residues: 64.9442 Evaluate side-chains 76 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 251 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.076450 restraints weight = 7281.205| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.39 r_work: 0.2812 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4368 Z= 0.124 Angle : 0.524 5.323 5840 Z= 0.277 Chirality : 0.033 0.190 634 Planarity : 0.003 0.021 712 Dihedral : 8.015 58.451 688 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.39 % Allowed : 14.81 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.86 (0.38), residues: 506 helix: 3.98 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.60 (0.73), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 292 TYR 0.013 0.001 TYR U 195 PHE 0.007 0.001 PHE A 97 TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 4368) covalent geometry : angle 0.52380 / 0.28 ( 5840) hydrogen bonds : bond 0.04562 / 3.13 ( 328) hydrogen bonds : angle 2.78671 / 2.17 ( 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 81 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.171 Fit side-chains REVERT: U 51 GLN cc_start: 0.8809 (tp40) cc_final: 0.8525 (tm-30) REVERT: U 54 GLU cc_start: 0.8815 (tp30) cc_final: 0.8529 (tp30) REVERT: U 251 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.6911 (t80) REVERT: U 292 ARG cc_start: 0.8919 (ttm-80) cc_final: 0.8593 (ttm110) REVERT: A 51 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8523 (tm-30) REVERT: A 54 GLU cc_start: 0.8739 (tp30) cc_final: 0.8466 (tp30) REVERT: A 292 ARG cc_start: 0.8880 (ttm-80) cc_final: 0.8632 (ttm110) outliers start: 6 outliers final: 2 residues processed: 77 average time/residue: 0.8235 time to fit residues: 64.8365 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 : 0.168 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.074250 restraints weight = 7410.051| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.41 r_work: 0.2765 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 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 0.033 4368 Z= 0.141 Angle : 0.552 5.267 5840 Z= 0.293 Chirality : 0.034 0.185 634 Planarity : 0.003 0.022 712 Dihedral : 7.953 57.651 686 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.16 % Allowed : 16.20 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.81 (0.38), residues: 506 helix: 3.96 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.65 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 62 TYR 0.013 0.001 TYR U 195 PHE 0.010 0.001 PHE A 97 TRP 0.007 0.001 TRP U 53 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 4368) covalent geometry : angle 0.55224 / 0.29 ( 5840) hydrogen bonds : bond 0.04976 / 3.42 ( 328) hydrogen bonds : angle 2.87133 / 2.22 ( 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 79 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.165 Fit side-chains REVERT: U 51 GLN cc_start: 0.8827 (tp40) cc_final: 0.8522 (tm-30) REVERT: U 54 GLU cc_start: 0.8802 (tp30) cc_final: 0.8506 (tp30) REVERT: U 190 TRP cc_start: 0.8004 (m100) cc_final: 0.7690 (m-10) REVERT: U 196 TYR cc_start: 0.8055 (m-10) cc_final: 0.7848 (m-80) REVERT: U 251 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7000 (t80) REVERT: U 292 ARG cc_start: 0.8904 (ttm-80) cc_final: 0.8578 (ttm110) REVERT: A 51 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8537 (tm-30) REVERT: A 54 GLU cc_start: 0.8714 (tp30) cc_final: 0.8389 (tp30) REVERT: A 65 GLN cc_start: 0.8676 (pm20) cc_final: 0.8271 (mp10) REVERT: A 292 ARG cc_start: 0.8897 (ttm-80) cc_final: 0.8622 (ttm110) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.8460 time to fit residues: 64.9992 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 : 0.169 ------------------------------------------------------------------------------- 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: 0.8980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.073020 restraints weight = 7310.668| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.45 r_work: 0.2745 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4368 Z= 0.148 Angle : 0.564 5.629 5840 Z= 0.300 Chirality : 0.034 0.187 634 Planarity : 0.003 0.021 712 Dihedral : 7.791 56.942 686 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.16 % Allowed : 16.67 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.79 (0.38), residues: 506 helix: 3.95 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.66 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 62 TYR 0.012 0.001 TYR U 195 PHE 0.009 0.001 PHE U 232 TRP 0.008 0.001 TRP U 95 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 4368) covalent geometry : angle 0.56364 / 0.30 ( 5840) hydrogen bonds : bond 0.05120 / 3.51 ( 328) hydrogen bonds : angle 2.89903 / 2.24 ( 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 79 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.119 Fit side-chains REVERT: U 46 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8682 (tt0) REVERT: U 51 GLN cc_start: 0.8804 (tp40) cc_final: 0.8493 (tm-30) REVERT: U 54 GLU cc_start: 0.8771 (tp30) cc_final: 0.8442 (tp30) REVERT: U 190 TRP cc_start: 0.8076 (m100) cc_final: 0.7770 (m-10) REVERT: U 251 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.6983 (t80) REVERT: U 292 ARG cc_start: 0.8950 (ttm-80) cc_final: 0.8626 (ttm110) REVERT: A 51 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8525 (tm-30) REVERT: A 54 GLU cc_start: 0.8669 (tp30) cc_final: 0.8372 (tp30) REVERT: A 292 ARG cc_start: 0.8926 (ttm-80) cc_final: 0.8618 (ttm110) outliers start: 5 outliers final: 2 residues processed: 76 average time/residue: 0.8838 time to fit residues: 68.7962 Evaluate side-chains 76 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU 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: 2.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.0470 chunk 45 optimal weight: 0.0010 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.077104 restraints weight = 7162.251| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.43 r_work: 0.2819 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4368 Z= 0.125 Angle : 0.560 7.242 5840 Z= 0.295 Chirality : 0.033 0.200 634 Planarity : 0.003 0.023 712 Dihedral : 7.026 53.614 686 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.16 % Allowed : 17.36 % 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 are not related in a simple way. whole: 4.96 (0.38), residues: 506 helix: 4.06 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.61 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 292 TYR 0.012 0.001 TYR U 195 PHE 0.007 0.001 PHE A 97 TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 4368) covalent geometry : angle 0.55969 / 0.29 ( 5840) hydrogen bonds : bond 0.04307 / 2.95 ( 328) hydrogen bonds : angle 2.73196 / 2.12 ( 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 75 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.146 Fit side-chains REVERT: U 46 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8650 (tt0) REVERT: U 51 GLN cc_start: 0.8792 (tp40) cc_final: 0.8473 (tm-30) REVERT: U 54 GLU cc_start: 0.8777 (tp30) cc_final: 0.8449 (tp30) REVERT: U 190 TRP cc_start: 0.8131 (m100) cc_final: 0.7822 (m-10) REVERT: U 251 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.6928 (t80) REVERT: U 292 ARG cc_start: 0.8911 (ttm-80) cc_final: 0.8579 (ttm110) REVERT: A 51 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8473 (tm-30) REVERT: A 54 GLU cc_start: 0.8647 (tp30) cc_final: 0.8238 (tp30) REVERT: A 65 GLN cc_start: 0.8694 (pm20) cc_final: 0.8282 (mp10) REVERT: A 292 ARG cc_start: 0.8852 (ttm-80) cc_final: 0.8570 (ttm110) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.7854 time to fit residues: 58.8051 Evaluate side-chains 77 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.096260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.073791 restraints weight = 7379.522| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.43 r_work: 0.2760 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4368 Z= 0.154 Angle : 0.601 7.910 5840 Z= 0.320 Chirality : 0.034 0.195 634 Planarity : 0.003 0.025 712 Dihedral : 7.472 51.577 686 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.16 % Allowed : 17.36 % 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 are not related in a simple way. whole: 4.83 (0.38), residues: 506 helix: 3.98 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.70 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 292 TYR 0.010 0.001 TYR A 195 PHE 0.009 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/Z covalent geometry : bond 0.00355 / 0.15 ( 4368) covalent geometry : angle 0.60121 / 0.32 ( 5840) hydrogen bonds : bond 0.05035 / 3.46 ( 328) hydrogen bonds : angle 2.86894 / 2.22 ( 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 80 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.164 Fit side-chains REVERT: U 46 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8660 (tt0) REVERT: U 51 GLN cc_start: 0.8836 (tp40) cc_final: 0.8502 (tm-30) REVERT: U 54 GLU cc_start: 0.8790 (tp30) cc_final: 0.8462 (tp30) REVERT: U 190 TRP cc_start: 0.8130 (m100) cc_final: 0.7836 (m-10) REVERT: U 251 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.6963 (t80) REVERT: U 292 ARG cc_start: 0.8907 (ttm-80) cc_final: 0.8590 (ttm110) REVERT: A 51 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8528 (tm-30) REVERT: A 54 GLU cc_start: 0.8675 (tp30) cc_final: 0.8270 (tp30) REVERT: A 292 ARG cc_start: 0.8905 (ttm-80) cc_final: 0.8603 (ttm110) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.8317 time to fit residues: 65.6669 Evaluate side-chains 77 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.0570 chunk 33 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.075638 restraints weight = 7297.251| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.42 r_work: 0.2793 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.4635 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= 0.137 Angle : 0.595 8.607 5840 Z= 0.314 Chirality : 0.034 0.206 634 Planarity : 0.003 0.024 712 Dihedral : 7.133 48.715 686 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.16 % Allowed : 18.06 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.92 (0.38), residues: 506 helix: 4.03 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -0.61 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 292 TYR 0.011 0.001 TYR U 195 PHE 0.006 0.001 PHE A 97 TRP 0.007 0.001 TRP U 95 HIS 0.004 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 4368) covalent geometry : angle 0.59463 / 0.31 ( 5840) hydrogen bonds : bond 0.04595 / 3.15 ( 328) hydrogen bonds : angle 2.78122 / 2.16 ( 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 77 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.162 Fit side-chains REVERT: U 46 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8684 (tt0) REVERT: U 51 GLN cc_start: 0.8828 (tp40) cc_final: 0.8504 (tm-30) REVERT: U 54 GLU cc_start: 0.8785 (tp30) cc_final: 0.8459 (tp30) REVERT: U 190 TRP cc_start: 0.8080 (m100) cc_final: 0.7769 (m-10) REVERT: U 251 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.6982 (t80) REVERT: U 292 ARG cc_start: 0.8905 (ttm-80) cc_final: 0.8585 (ttm110) REVERT: A 51 GLN cc_start: 0.8790 (tp-100) cc_final: 0.8504 (tm-30) REVERT: A 54 GLU cc_start: 0.8666 (tp30) cc_final: 0.8264 (tp30) REVERT: A 65 GLN cc_start: 0.8584 (pm20) cc_final: 0.8163 (mp10) REVERT: A 292 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8580 (ttm110) outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 0.8279 time to fit residues: 62.8101 Evaluate side-chains 77 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.071209 restraints weight = 7240.185| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.46 r_work: 0.2722 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4368 Z= 0.170 Angle : 0.629 8.406 5840 Z= 0.335 Chirality : 0.035 0.189 634 Planarity : 0.003 0.025 712 Dihedral : 7.720 49.769 686 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.93 % Allowed : 18.75 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.76 (0.38), residues: 506 helix: 3.92 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -0.69 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 292 TYR 0.011 0.001 TYR A 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/Z covalent geometry : bond 0.00399 / 0.17 ( 4368) covalent geometry : angle 0.62892 / 0.33 ( 5840) hydrogen bonds : bond 0.05322 / 3.66 ( 328) hydrogen bonds : angle 2.94092 / 2.27 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.67 seconds wall clock time: 37 minutes 26.15 seconds (2246.15 seconds total)