Starting phenix.real_space_refine on Sat May 10 02:11:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bws_44978/05_2025/9bws_44978_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bws_44978/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bws_44978/05_2025/9bws_44978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bws_44978/05_2025/9bws_44978.map" model { file = "/net/cci-nas-00/data/ceres_data/9bws_44978/05_2025/9bws_44978_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bws_44978/05_2025/9bws_44978_trim.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.61, per 1000 atoms: 0.84 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: 1.21 Conformation dependent library (CDL) restraints added in 464.5 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: 0.35 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: 1.09 Time building geometry restraints manager: 1.32 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.002 TRP U 53 HIS 0.004 0.001 HIS U 77 PHE 0.010 0.002 PHE A 232 TYR 0.009 0.001 TYR U 216 ARG 0.020 0.001 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.10917 ( 328) hydrogen bonds : angle 3.69557 ( 984) covalent geometry : bond 0.00391 ( 4368) covalent geometry : angle 0.67652 ( 5840) *********************** 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 : 0.455 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: 1.3596 time to fit residues: 158.1126 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 : 0.482 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.099729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077830 restraints weight = 7287.639| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.41 r_work: 0.2829 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4368 Z= 0.136 Angle : 0.531 5.178 5840 Z= 0.289 Chirality : 0.034 0.172 634 Planarity : 0.003 0.024 712 Dihedral : 9.670 58.817 691 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.31 % Allowed : 15.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.53 (0.38), residues: 506 helix: 3.76 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.73 (0.70), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 95 HIS 0.004 0.001 HIS U 64 PHE 0.009 0.001 PHE U 232 TYR 0.018 0.001 TYR U 195 ARG 0.004 0.001 ARG U 148 Details of bonding type rmsd hydrogen bonds : bond 0.04980 ( 328) hydrogen bonds : angle 2.93690 ( 984) covalent geometry : bond 0.00291 ( 4368) covalent geometry : angle 0.53138 ( 5840) *********************** 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 100 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.477 Fit side-chains REVERT: U 54 GLU cc_start: 0.8776 (tp30) cc_final: 0.8466 (tp30) REVERT: U 220 GLU cc_start: 0.8319 (pt0) cc_final: 0.7963 (pt0) REVERT: U 251 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.6954 (t80) REVERT: A 54 GLU cc_start: 0.8807 (tp30) cc_final: 0.8556 (tp30) REVERT: A 62 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8281 (ttp-110) REVERT: A 251 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.6672 (t80) outliers start: 10 outliers final: 2 residues processed: 96 average time/residue: 1.5353 time to fit residues: 151.4311 Evaluate side-chains 84 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 43 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.097138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.075042 restraints weight = 7167.157| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.37 r_work: 0.2780 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4368 Z= 0.134 Angle : 0.537 7.474 5840 Z= 0.281 Chirality : 0.033 0.181 634 Planarity : 0.003 0.025 712 Dihedral : 8.679 56.709 688 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.39 % Allowed : 16.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.74 (0.38), residues: 506 helix: 3.89 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.55 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 95 HIS 0.003 0.001 HIS U 64 PHE 0.008 0.001 PHE A 232 TYR 0.008 0.001 TYR U 78 ARG 0.005 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.04950 ( 328) hydrogen bonds : angle 2.87575 ( 984) covalent geometry : bond 0.00288 ( 4368) covalent geometry : angle 0.53657 ( 5840) *********************** 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 86 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.470 Fit side-chains REVERT: U 51 GLN cc_start: 0.8826 (tp40) cc_final: 0.8613 (tm-30) REVERT: U 54 GLU cc_start: 0.8772 (tp30) cc_final: 0.8390 (tp30) REVERT: U 220 GLU cc_start: 0.8347 (pt0) cc_final: 0.8010 (pt0) REVERT: U 251 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7020 (t80) REVERT: A 54 GLU cc_start: 0.8724 (tp30) cc_final: 0.8449 (tp30) outliers start: 6 outliers final: 2 residues processed: 82 average time/residue: 1.6182 time to fit residues: 136.2810 Evaluate side-chains 79 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 0.0570 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.097555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.075584 restraints weight = 7298.247| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.40 r_work: 0.2780 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4143 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= 0.128 Angle : 0.537 6.624 5840 Z= 0.282 Chirality : 0.033 0.184 634 Planarity : 0.003 0.024 712 Dihedral : 8.032 59.037 686 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.78 (0.38), residues: 506 helix: 3.93 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.64 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 95 HIS 0.001 0.000 HIS A 77 PHE 0.008 0.001 PHE A 97 TYR 0.014 0.001 TYR U 195 ARG 0.007 0.001 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.04739 ( 328) hydrogen bonds : angle 2.80650 ( 984) covalent geometry : bond 0.00276 ( 4368) covalent geometry : angle 0.53672 ( 5840) *********************** 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 83 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.493 Fit side-chains REVERT: U 51 GLN cc_start: 0.8801 (tp40) cc_final: 0.8550 (tm-30) REVERT: U 54 GLU cc_start: 0.8768 (tp30) cc_final: 0.8527 (tp30) REVERT: U 251 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.6935 (t80) REVERT: U 292 ARG cc_start: 0.8982 (ttm-80) cc_final: 0.8620 (ttm110) REVERT: A 54 GLU cc_start: 0.8709 (tp30) cc_final: 0.8369 (tp30) REVERT: A 292 ARG cc_start: 0.8934 (ttm-80) cc_final: 0.8641 (ttm110) outliers start: 6 outliers final: 1 residues processed: 79 average time/residue: 1.6187 time to fit residues: 131.2988 Evaluate side-chains 72 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.096033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.073851 restraints weight = 7320.724| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.41 r_work: 0.2742 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4368 Z= 0.142 Angle : 0.544 6.963 5840 Z= 0.287 Chirality : 0.034 0.189 634 Planarity : 0.003 0.022 712 Dihedral : 8.113 58.883 686 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.62 % Allowed : 14.12 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.72 (0.38), residues: 506 helix: 3.91 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.77 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 53 HIS 0.001 0.000 HIS A 64 PHE 0.008 0.001 PHE A 97 TYR 0.013 0.001 TYR U 195 ARG 0.004 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 328) hydrogen bonds : angle 2.88358 ( 984) covalent geometry : bond 0.00316 ( 4368) covalent geometry : angle 0.54382 ( 5840) *********************** 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 83 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.480 Fit side-chains REVERT: U 51 GLN cc_start: 0.8803 (tp40) cc_final: 0.8532 (tm-30) REVERT: U 54 GLU cc_start: 0.8771 (tp30) cc_final: 0.8333 (tp30) REVERT: U 251 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.6975 (t80) REVERT: U 292 ARG cc_start: 0.8959 (ttm-80) cc_final: 0.8593 (ttm110) REVERT: A 51 GLN cc_start: 0.8803 (tp40) cc_final: 0.8590 (tm-30) REVERT: A 54 GLU cc_start: 0.8681 (tp30) cc_final: 0.8252 (tp30) REVERT: A 292 ARG cc_start: 0.8920 (ttm-80) cc_final: 0.8612 (ttm110) outliers start: 7 outliers final: 2 residues processed: 77 average time/residue: 1.5970 time to fit residues: 126.2507 Evaluate side-chains 77 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.099356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.076858 restraints weight = 7278.491| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.41 r_work: 0.2822 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4368 Z= 0.118 Angle : 0.521 5.426 5840 Z= 0.275 Chirality : 0.033 0.196 634 Planarity : 0.003 0.020 712 Dihedral : 7.220 55.401 686 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.93 % Allowed : 16.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.38), residues: 506 helix: 4.04 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.78 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.006 0.001 PHE A 97 TYR 0.014 0.001 TYR U 195 ARG 0.004 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 328) hydrogen bonds : angle 2.69572 ( 984) covalent geometry : bond 0.00249 ( 4368) covalent geometry : angle 0.52105 ( 5840) *********************** 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 86 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.454 Fit side-chains REVERT: U 51 GLN cc_start: 0.8781 (tp40) cc_final: 0.8499 (tm-30) REVERT: U 54 GLU cc_start: 0.8774 (tp30) cc_final: 0.8333 (tp30) REVERT: U 190 TRP cc_start: 0.8011 (m100) cc_final: 0.7701 (m-10) REVERT: U 251 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.6874 (t80) REVERT: U 292 ARG cc_start: 0.8923 (ttm-80) cc_final: 0.8593 (ttm110) REVERT: A 51 GLN cc_start: 0.8836 (tp40) cc_final: 0.8588 (tm-30) REVERT: A 54 GLU cc_start: 0.8689 (tp30) cc_final: 0.8258 (tp30) REVERT: A 292 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8570 (ttm110) outliers start: 4 outliers final: 2 residues processed: 83 average time/residue: 1.6895 time to fit residues: 143.7321 Evaluate side-chains 80 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 43 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.099788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.077301 restraints weight = 7321.353| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.42 r_work: 0.2814 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4483 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= 0.123 Angle : 0.541 6.257 5840 Z= 0.285 Chirality : 0.033 0.200 634 Planarity : 0.003 0.020 712 Dihedral : 6.967 53.750 686 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.69 % Allowed : 17.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.89 (0.38), residues: 506 helix: 4.05 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.81 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 53 HIS 0.001 0.000 HIS A 64 PHE 0.006 0.001 PHE A 232 TYR 0.012 0.001 TYR U 195 ARG 0.004 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 328) hydrogen bonds : angle 2.69714 ( 984) covalent geometry : bond 0.00266 ( 4368) covalent geometry : angle 0.54076 ( 5840) *********************** 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: 3 poor density : 75 time to evaluate : 0.505 Fit side-chains REVERT: U 51 GLN cc_start: 0.8840 (tp40) cc_final: 0.8538 (tm-30) REVERT: U 54 GLU cc_start: 0.8801 (tp30) cc_final: 0.8317 (tp30) REVERT: U 190 TRP cc_start: 0.8015 (m100) cc_final: 0.7702 (m-10) REVERT: U 251 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.6842 (t80) REVERT: U 292 ARG cc_start: 0.8909 (ttm-80) cc_final: 0.8593 (ttm110) REVERT: A 51 GLN cc_start: 0.8830 (tp40) cc_final: 0.8555 (tm-30) REVERT: A 54 GLU cc_start: 0.8704 (tp30) cc_final: 0.8258 (tp30) REVERT: A 65 GLN cc_start: 0.8666 (pm20) cc_final: 0.8218 (mp10) REVERT: A 292 ARG cc_start: 0.8862 (ttm-80) cc_final: 0.8570 (ttm110) outliers start: 3 outliers final: 3 residues processed: 77 average time/residue: 1.5605 time to fit residues: 123.6159 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 : 0.451 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 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 = 0.3284 r_free = 0.3284 target = 0.096264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.073823 restraints weight = 7242.802| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.40 r_work: 0.2761 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4530 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= 0.143 Angle : 0.569 6.841 5840 Z= 0.302 Chirality : 0.034 0.197 634 Planarity : 0.003 0.021 712 Dihedral : 7.253 53.943 686 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.69 % Allowed : 18.29 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.82 (0.38), residues: 506 helix: 4.00 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.82 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.002 0.001 HIS A 64 PHE 0.010 0.001 PHE A 97 TYR 0.013 0.001 TYR U 195 ARG 0.003 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 328) hydrogen bonds : angle 2.80748 ( 984) covalent geometry : bond 0.00322 ( 4368) covalent geometry : angle 0.56925 ( 5840) *********************** 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: 3 poor density : 75 time to evaluate : 0.452 Fit side-chains REVERT: U 51 GLN cc_start: 0.8824 (tp40) cc_final: 0.8513 (tm-30) REVERT: U 54 GLU cc_start: 0.8787 (tp30) cc_final: 0.8340 (tp30) REVERT: U 65 GLN cc_start: 0.8736 (pm20) cc_final: 0.8481 (mp10) REVERT: U 190 TRP cc_start: 0.8014 (m100) cc_final: 0.7705 (m-10) REVERT: U 251 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.6939 (t80) REVERT: U 292 ARG cc_start: 0.8947 (ttm-80) cc_final: 0.8634 (ttm110) REVERT: A 51 GLN cc_start: 0.8862 (tp40) cc_final: 0.8574 (tm-30) REVERT: A 54 GLU cc_start: 0.8687 (tp30) cc_final: 0.8258 (tp30) REVERT: A 292 ARG cc_start: 0.8915 (ttm-80) cc_final: 0.8610 (ttm110) outliers start: 3 outliers final: 2 residues processed: 76 average time/residue: 1.6335 time to fit residues: 127.5452 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 : 0.424 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.094977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.072416 restraints weight = 7363.365| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.43 r_work: 0.2739 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4368 Z= 0.154 Angle : 0.595 7.926 5840 Z= 0.316 Chirality : 0.034 0.192 634 Planarity : 0.003 0.023 712 Dihedral : 7.539 53.358 686 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.69 % Allowed : 18.29 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.74 (0.38), residues: 506 helix: 3.94 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.84 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.005 0.001 HIS A 64 PHE 0.009 0.001 PHE A 97 TYR 0.010 0.001 TYR A 195 ARG 0.003 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.05164 ( 328) hydrogen bonds : angle 2.88488 ( 984) covalent geometry : bond 0.00354 ( 4368) covalent geometry : angle 0.59489 ( 5840) *********************** 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 78 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.489 Fit side-chains REVERT: U 51 GLN cc_start: 0.8853 (tp40) cc_final: 0.8556 (tm-30) REVERT: U 54 GLU cc_start: 0.8779 (tp30) cc_final: 0.8349 (tp30) REVERT: U 190 TRP cc_start: 0.8083 (m100) cc_final: 0.7799 (m-10) REVERT: U 251 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.6943 (t80) REVERT: U 292 ARG cc_start: 0.8930 (ttm-80) cc_final: 0.8602 (ttm110) REVERT: A 51 GLN cc_start: 0.8881 (tp40) cc_final: 0.8582 (tm-30) REVERT: A 54 GLU cc_start: 0.8694 (tp30) cc_final: 0.8261 (tp30) REVERT: A 65 GLN cc_start: 0.8710 (pm20) cc_final: 0.8395 (mp10) REVERT: A 292 ARG cc_start: 0.8928 (ttm-80) cc_final: 0.8609 (ttm110) REVERT: A 293 LYS cc_start: 0.8592 (tppp) cc_final: 0.8269 (tppt) outliers start: 3 outliers final: 2 residues processed: 76 average time/residue: 1.6013 time to fit residues: 124.9252 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 : 0.454 ------------------------------------------------------------------------------- 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 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.095600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.072938 restraints weight = 7156.382| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.40 r_work: 0.2749 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4368 Z= 0.149 Angle : 0.607 8.427 5840 Z= 0.322 Chirality : 0.035 0.199 634 Planarity : 0.003 0.026 712 Dihedral : 7.462 50.712 686 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.69 % Allowed : 18.29 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.75 (0.38), residues: 506 helix: 3.94 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.81 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 53 HIS 0.002 0.001 HIS A 64 PHE 0.010 0.001 PHE A 97 TYR 0.011 0.001 TYR U 195 ARG 0.005 0.000 ARG U 62 Details of bonding type rmsd hydrogen bonds : bond 0.05018 ( 328) hydrogen bonds : angle 2.85470 ( 984) covalent geometry : bond 0.00341 ( 4368) covalent geometry : angle 0.60739 ( 5840) ********************** 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: 3 poor density : 74 time to evaluate : 0.458 Fit side-chains REVERT: U 51 GLN cc_start: 0.8845 (tp40) cc_final: 0.8540 (tm-30) REVERT: U 54 GLU cc_start: 0.8761 (tp30) cc_final: 0.8333 (tp30) REVERT: U 65 GLN cc_start: 0.8749 (pm20) cc_final: 0.8402 (mp10) REVERT: U 190 TRP cc_start: 0.8073 (m100) cc_final: 0.7790 (m-10) REVERT: U 251 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.6945 (t80) REVERT: U 292 ARG cc_start: 0.8931 (ttm-80) cc_final: 0.8602 (ttm110) REVERT: A 51 GLN cc_start: 0.8879 (tp40) cc_final: 0.8587 (tm-30) REVERT: A 54 GLU cc_start: 0.8659 (tp30) cc_final: 0.8233 (tp30) REVERT: A 65 GLN cc_start: 0.8703 (pm20) cc_final: 0.8333 (mp10) REVERT: A 292 ARG cc_start: 0.8914 (ttm-80) cc_final: 0.8613 (ttm110) REVERT: A 293 LYS cc_start: 0.8583 (tppp) cc_final: 0.8379 (tmtt) outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 1.6007 time to fit residues: 123.2208 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 : 0.432 ------------------------------------------------------------------------------- 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 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.095960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.073367 restraints weight = 7298.152| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.40 r_work: 0.2742 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4618 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= 0.150 Angle : 0.605 8.719 5840 Z= 0.321 Chirality : 0.034 0.195 634 Planarity : 0.003 0.024 712 Dihedral : 7.497 49.932 686 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.69 % Allowed : 18.29 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.73 (0.38), residues: 506 helix: 3.93 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -0.81 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 PHE 0.008 0.001 PHE A 97 TYR 0.011 0.001 TYR A 195 ARG 0.008 0.000 ARG U 62 Details of bonding type rmsd hydrogen bonds : bond 0.05077 ( 328) hydrogen bonds : angle 2.87610 ( 984) covalent geometry : bond 0.00345 ( 4368) covalent geometry : angle 0.60507 ( 5840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4233.90 seconds wall clock time: 73 minutes 14.68 seconds (4394.68 seconds total)