Starting phenix.real_space_refine on Wed Jul 1 21:07:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0e_35900/07_2026/8j0e_35900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0e_35900/07_2026/8j0e_35900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j0e_35900/07_2026/8j0e_35900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0e_35900/07_2026/8j0e_35900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j0e_35900/07_2026/8j0e_35900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0e_35900/07_2026/8j0e_35900.map" } resolution = 3.4 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 9 5.16 5 C 1570 2.51 5 N 448 2.21 5 O 476 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: 2507 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 147 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "B" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2067 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 5, 'TRANS': 263} Chain breaks: 2 Chain: "E" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {' MG': 1, 'TKC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.76, per 1000 atoms: 0.30 Number of scatterers: 2507 At special positions: 0 Unit cell: (73.14, 68.9, 79.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 9 16.00 P 3 15.00 Mg 1 11.99 O 476 8.00 N 448 7.00 C 1570 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: 0.23 Conformation dependent library (CDL) restraints added in 90.0 milliseconds 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 586 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 61.4% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'F' and resid 72 through 78 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'B' and resid 6 through 14 removed outlier: 4.524A pdb=" N PHE B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA B 11 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 12 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.852A pdb=" N ARG B 32 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 Processing helix chain 'B' and resid 61 through 78 removed outlier: 3.533A pdb=" N LEU B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 91 through 114 removed outlier: 4.155A pdb=" N SER B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 3.690A pdb=" N ARG B 129 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 4.291A pdb=" N SER B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 188 Processing helix chain 'B' and resid 238 through 252 removed outlier: 3.551A pdb=" N VAL B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 281 through 285 removed outlier: 4.071A pdb=" N HIS B 285 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 78 Processing helix chain 'E' and resid 79 through 84 Processing sheet with id=AA1, first strand: chain 'B' and resid 118 through 123 removed outlier: 6.440A pdb=" N ALA B 119 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASN B 154 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET B 121 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL B 55 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N PHE B 153 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 57 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N GLU B 155 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG B 16 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE B 193 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 18 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU B 195 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS B 20 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 192 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR B 259 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU B 194 " --> pdb=" O THR B 259 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 330 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: 0.32 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 415 1.31 - 1.43: 635 1.43 - 1.55: 1465 1.55 - 1.68: 8 1.68 - 1.80: 16 Bond restraints: 2539 Sorted by residual: bond pdb=" C37 TKC B 801 " pdb=" C39 TKC B 801 " ideal model delta sigma weight residual 1.525 1.290 0.235 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C11 TKC B 801 " pdb=" O12 TKC B 801 " ideal model delta sigma weight residual 1.394 1.542 -0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C02 TKC B 801 " pdb=" N01 TKC B 801 " ideal model delta sigma weight residual 1.334 1.457 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C13 TKC B 801 " pdb=" O12 TKC B 801 " ideal model delta sigma weight residual 1.425 1.312 0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" C13 TKC B 801 " pdb=" C37 TKC B 801 " ideal model delta sigma weight residual 1.526 1.633 -0.107 2.00e-02 2.50e+03 2.87e+01 ... (remaining 2534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3391 4.85 - 9.71: 19 9.71 - 14.56: 5 14.56 - 19.42: 0 19.42 - 24.27: 3 Bond angle restraints: 3418 Sorted by residual: angle pdb=" N10 TKC B 801 " pdb=" C11 TKC B 801 " pdb=" O12 TKC B 801 " ideal model delta sigma weight residual 110.34 86.07 24.27 3.00e+00 1.11e-01 6.55e+01 angle pdb=" C39 TKC B 801 " pdb=" C11 TKC B 801 " pdb=" N10 TKC B 801 " ideal model delta sigma weight residual 114.15 136.18 -22.03 3.00e+00 1.11e-01 5.39e+01 angle pdb=" O23 TKC B 801 " pdb=" P24 TKC B 801 " pdb=" O27 TKC B 801 " ideal model delta sigma weight residual 90.60 110.07 -19.47 3.00e+00 1.11e-01 4.21e+01 angle pdb=" N LEU B 83 " pdb=" CA LEU B 83 " pdb=" C LEU B 83 " ideal model delta sigma weight residual 111.33 105.26 6.07 1.21e+00 6.83e-01 2.51e+01 angle pdb=" N LEU E 83 " pdb=" CA LEU E 83 " pdb=" C LEU E 83 " ideal model delta sigma weight residual 113.01 107.00 6.01 1.20e+00 6.94e-01 2.51e+01 ... (remaining 3413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.62: 1387 13.62 - 27.24: 130 27.24 - 40.85: 37 40.85 - 54.47: 8 54.47 - 68.09: 8 Dihedral angle restraints: 1570 sinusoidal: 665 harmonic: 905 Sorted by residual: dihedral pdb=" CA TYR B 251 " pdb=" C TYR B 251 " pdb=" N GLY B 252 " pdb=" CA GLY B 252 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ARG A 71 " pdb=" CB ARG A 71 " pdb=" CG ARG A 71 " pdb=" CD ARG A 71 " ideal model delta sinusoidal sigma weight residual 180.00 121.09 58.91 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLU B 108 " pdb=" CB GLU B 108 " pdb=" CG GLU B 108 " pdb=" CD GLU B 108 " ideal model delta sinusoidal sigma weight residual -180.00 -122.07 -57.93 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 291 0.042 - 0.084: 70 0.084 - 0.126: 25 0.126 - 0.168: 1 0.168 - 0.210: 2 Chirality restraints: 389 Sorted by residual: chirality pdb=" C39 TKC B 801 " pdb=" C11 TKC B 801 " pdb=" C37 TKC B 801 " pdb=" O40 TKC B 801 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C37 TKC B 801 " pdb=" C13 TKC B 801 " pdb=" C39 TKC B 801 " pdb=" O38 TKC B 801 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE B 257 " pdb=" N ILE B 257 " pdb=" C ILE B 257 " pdb=" CB ILE B 257 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 386 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 77 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ASN F 77 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN F 77 " 0.009 2.00e-02 2.50e+03 pdb=" N SER F 78 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 85 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO B 86 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 251 " 0.010 2.00e-02 2.50e+03 6.38e-03 8.14e-01 pdb=" CG TYR B 251 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR B 251 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 251 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 251 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 251 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 251 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 251 " 0.001 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 610 2.79 - 3.31: 2410 3.31 - 3.84: 3951 3.84 - 4.37: 4563 4.37 - 4.90: 7740 Nonbonded interactions: 19274 Sorted by model distance: nonbonded pdb=" NZ LYS B 15 " pdb=" O GLY B 52 " model vdw 2.257 3.120 nonbonded pdb=" O GLY B 237 " pdb="MG MG B 802 " model vdw 2.266 2.170 nonbonded pdb=" OD2 ASP B 208 " pdb=" OG1 THR B 210 " model vdw 2.269 3.040 nonbonded pdb=" O26 TKC B 801 " pdb="MG MG B 802 " model vdw 2.300 2.170 nonbonded pdb=" N GLY B 61 " pdb=" O36 TKC B 801 " model vdw 2.325 3.120 ... (remaining 19269 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 71 through 85) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.020 Find NCS groups from input model: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.009 0.235 2539 Z= 0.489 Angle : 1.133 24.272 3418 Z= 0.515 Chirality : 0.044 0.210 389 Planarity : 0.003 0.032 432 Dihedral : 12.587 68.086 984 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.64 % Allowed : 7.92 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.51), residues: 304 helix: 0.19 (0.40), residues: 179 sheet: 0.70 (0.91), residues: 42 loop : 0.11 (0.77), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 73 TYR 0.015 0.002 TYR B 251 PHE 0.009 0.001 PHE B 228 TRP 0.002 0.001 TRP B 287 HIS 0.001 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00914 / 0.49 ( 2539) covalent geometry : angle 1.13260 / 0.52 ( 3418) hydrogen bonds : bond 0.20215 / 13.24 ( 119) hydrogen bonds : angle 6.30984 / 4.18 ( 330) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.060 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8548 (tpt90) cc_final: 0.8013 (mtt180) REVERT: A 78 SER cc_start: 0.9240 (m) cc_final: 0.8939 (t) REVERT: A 83 LEU cc_start: 0.9249 (mm) cc_final: 0.8964 (mm) REVERT: B 54 GLU cc_start: 0.8068 (mp0) cc_final: 0.7677 (mp0) REVERT: B 80 PHE cc_start: 0.9085 (t80) cc_final: 0.8815 (t80) REVERT: E 75 LEU cc_start: 0.9150 (mp) cc_final: 0.8866 (mp) outliers start: 7 outliers final: 4 residues processed: 105 average time/residue: 0.0615 time to fit residues: 7.3639 Evaluate side-chains 78 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 278 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.114537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089436 restraints weight = 4696.141| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.09 r_work: 0.3005 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2539 Z= 0.146 Angle : 0.543 5.935 3418 Z= 0.270 Chirality : 0.041 0.151 389 Planarity : 0.003 0.024 432 Dihedral : 9.072 59.176 401 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.64 % Allowed : 12.45 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.51), residues: 304 helix: 0.97 (0.40), residues: 180 sheet: 0.69 (0.87), residues: 42 loop : 0.05 (0.75), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.016 0.002 TYR E 72 PHE 0.015 0.002 PHE B 228 TRP 0.002 0.001 TRP B 174 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 2539) covalent geometry : angle 0.54266 / 0.27 ( 3418) hydrogen bonds : bond 0.03853 / 2.43 ( 119) hydrogen bonds : angle 4.48595 / 3.03 ( 330) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.095 Fit side-chains REVERT: F 77 ASN cc_start: 0.9005 (m-40) cc_final: 0.8697 (t0) REVERT: A 73 ARG cc_start: 0.8518 (tpt90) cc_final: 0.7902 (mtt180) REVERT: A 78 SER cc_start: 0.9437 (m) cc_final: 0.9002 (t) REVERT: A 83 LEU cc_start: 0.9419 (mm) cc_final: 0.9161 (mm) REVERT: B 54 GLU cc_start: 0.8740 (mp0) cc_final: 0.7673 (mp0) REVERT: B 82 ASP cc_start: 0.9607 (m-30) cc_final: 0.9372 (m-30) REVERT: B 174 TRP cc_start: 0.5751 (OUTLIER) cc_final: 0.3365 (t-100) outliers start: 7 outliers final: 2 residues processed: 85 average time/residue: 0.0749 time to fit residues: 7.3223 Evaluate side-chains 77 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 176 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.087988 restraints weight = 4834.120| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.16 r_work: 0.2988 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2539 Z= 0.156 Angle : 0.524 6.146 3418 Z= 0.265 Chirality : 0.041 0.138 389 Planarity : 0.003 0.025 432 Dihedral : 8.097 57.478 398 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.40 % Allowed : 13.58 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.30 (0.50), residues: 304 helix: 1.37 (0.40), residues: 180 sheet: 0.42 (0.83), residues: 42 loop : 0.18 (0.72), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 6 TYR 0.013 0.002 TYR F 72 PHE 0.015 0.001 PHE B 280 TRP 0.002 0.001 TRP B 174 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 2539) covalent geometry : angle 0.52405 / 0.26 ( 3418) hydrogen bonds : bond 0.03551 / 2.34 ( 119) hydrogen bonds : angle 4.12982 / 2.85 ( 330) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.104 Fit side-chains REVERT: F 77 ASN cc_start: 0.9113 (m-40) cc_final: 0.8784 (t0) REVERT: A 72 TYR cc_start: 0.8508 (t80) cc_final: 0.8303 (t80) REVERT: A 73 ARG cc_start: 0.8547 (tpt90) cc_final: 0.7806 (mtt180) REVERT: A 78 SER cc_start: 0.9462 (m) cc_final: 0.9012 (t) REVERT: A 83 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9127 (mm) REVERT: B 54 GLU cc_start: 0.8769 (mp0) cc_final: 0.7710 (mp0) REVERT: B 82 ASP cc_start: 0.9593 (m-30) cc_final: 0.9266 (m-30) REVERT: B 108 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8311 (tm-30) REVERT: B 110 MET cc_start: 0.7692 (mmm) cc_final: 0.7377 (tpt) REVERT: B 147 MET cc_start: 0.8948 (tpp) cc_final: 0.8574 (tpt) REVERT: B 174 TRP cc_start: 0.6138 (OUTLIER) cc_final: 0.3419 (t-100) REVERT: B 287 TRP cc_start: 0.7950 (OUTLIER) cc_final: 0.7633 (m-10) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.0762 time to fit residues: 7.6671 Evaluate side-chains 89 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 TRP Chi-restraints excluded: chain E residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.0040 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090135 restraints weight = 4678.989| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.16 r_work: 0.3020 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2539 Z= 0.110 Angle : 0.488 6.937 3418 Z= 0.246 Chirality : 0.040 0.135 389 Planarity : 0.002 0.018 432 Dihedral : 7.920 57.527 398 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.40 % Allowed : 13.96 % 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: 1.65 (0.50), residues: 304 helix: 1.62 (0.40), residues: 180 sheet: 0.42 (0.82), residues: 42 loop : 0.47 (0.72), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 6 TYR 0.016 0.001 TYR F 72 PHE 0.014 0.001 PHE B 280 TRP 0.006 0.001 TRP B 287 HIS 0.001 0.000 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 2539) covalent geometry : angle 0.48834 / 0.25 ( 3418) hydrogen bonds : bond 0.02893 / 1.89 ( 119) hydrogen bonds : angle 3.91037 / 2.71 ( 330) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: F 77 ASN cc_start: 0.9063 (m-40) cc_final: 0.8785 (t0) REVERT: A 73 ARG cc_start: 0.8563 (tpt90) cc_final: 0.7872 (mtt180) REVERT: A 78 SER cc_start: 0.9463 (m) cc_final: 0.9025 (t) REVERT: A 83 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9157 (mm) REVERT: B 82 ASP cc_start: 0.9568 (m-30) cc_final: 0.9345 (m-30) REVERT: B 108 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8175 (tm-30) REVERT: B 110 MET cc_start: 0.7876 (mmm) cc_final: 0.7457 (tpt) REVERT: B 147 MET cc_start: 0.8784 (tpp) cc_final: 0.8550 (tpt) REVERT: B 174 TRP cc_start: 0.6355 (OUTLIER) cc_final: 0.3309 (t-100) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.0735 time to fit residues: 6.9332 Evaluate side-chains 81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain E residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 23 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089125 restraints weight = 4721.047| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.16 r_work: 0.2998 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2539 Z= 0.135 Angle : 0.503 7.024 3418 Z= 0.253 Chirality : 0.040 0.135 389 Planarity : 0.002 0.018 432 Dihedral : 7.966 59.980 398 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.77 % Allowed : 16.23 % Favored : 80.00 % 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: 1.67 (0.50), residues: 304 helix: 1.70 (0.41), residues: 180 sheet: 0.37 (0.82), residues: 42 loop : 0.38 (0.70), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.016 0.001 TYR F 72 PHE 0.024 0.002 PHE F 80 TRP 0.012 0.002 TRP B 287 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 2539) covalent geometry : angle 0.50332 / 0.25 ( 3418) hydrogen bonds : bond 0.03199 / 2.12 ( 119) hydrogen bonds : angle 3.85913 / 2.64 ( 330) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.068 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.5531 (ptt-90) cc_final: 0.3263 (ptt180) REVERT: A 71 ARG cc_start: 0.7036 (mpp-170) cc_final: 0.6387 (mpp-170) REVERT: A 73 ARG cc_start: 0.8615 (tpt90) cc_final: 0.7893 (mtt180) REVERT: A 78 SER cc_start: 0.9503 (m) cc_final: 0.8898 (t) REVERT: A 83 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9074 (mm) REVERT: B 82 ASP cc_start: 0.9545 (m-30) cc_final: 0.9309 (m-30) REVERT: B 108 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 110 MET cc_start: 0.7966 (mmm) cc_final: 0.7566 (tpt) REVERT: B 147 MET cc_start: 0.8911 (tpp) cc_final: 0.8697 (tpt) REVERT: B 174 TRP cc_start: 0.6384 (OUTLIER) cc_final: 0.3229 (t-100) REVERT: E 79 SER cc_start: 0.8966 (p) cc_final: 0.8225 (t) outliers start: 10 outliers final: 6 residues processed: 84 average time/residue: 0.0686 time to fit residues: 6.6757 Evaluate side-chains 81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain E residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.0030 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 77 ASN B 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.116837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091481 restraints weight = 4745.631| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.17 r_work: 0.3037 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2539 Z= 0.105 Angle : 0.484 7.065 3418 Z= 0.248 Chirality : 0.040 0.133 389 Planarity : 0.002 0.018 432 Dihedral : 7.835 59.669 398 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.53 % Allowed : 14.72 % Favored : 80.75 % 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: 1.64 (0.50), residues: 304 helix: 1.68 (0.41), residues: 180 sheet: 0.39 (0.80), residues: 42 loop : 0.32 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 146 TYR 0.018 0.001 TYR F 72 PHE 0.021 0.001 PHE F 80 TRP 0.013 0.002 TRP B 287 HIS 0.001 0.000 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 2539) covalent geometry : angle 0.48447 / 0.25 ( 3418) hydrogen bonds : bond 0.02708 / 1.77 ( 119) hydrogen bonds : angle 3.82108 / 2.62 ( 330) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.5530 (OUTLIER) cc_final: 0.3268 (ptt180) REVERT: A 73 ARG cc_start: 0.8674 (tpt90) cc_final: 0.7889 (mtt180) REVERT: A 78 SER cc_start: 0.9458 (m) cc_final: 0.8887 (t) REVERT: A 83 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9088 (mm) REVERT: B 82 ASP cc_start: 0.9537 (m-30) cc_final: 0.9280 (m-30) REVERT: B 108 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8158 (tm-30) REVERT: B 110 MET cc_start: 0.7965 (mmm) cc_final: 0.7606 (tpt) REVERT: B 147 MET cc_start: 0.8764 (tpp) cc_final: 0.8543 (tpt) REVERT: B 174 TRP cc_start: 0.6591 (OUTLIER) cc_final: 0.3146 (t-100) REVERT: E 79 SER cc_start: 0.9022 (p) cc_final: 0.8625 (t) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.0666 time to fit residues: 6.6719 Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 27 optimal weight: 0.0870 chunk 23 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 77 ASN B 44 GLN B 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.121459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096666 restraints weight = 4535.205| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.07 r_work: 0.3146 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2539 Z= 0.105 Angle : 0.545 12.234 3418 Z= 0.268 Chirality : 0.040 0.136 389 Planarity : 0.002 0.015 432 Dihedral : 7.771 58.905 398 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.77 % Allowed : 16.60 % Favored : 79.62 % 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: 1.57 (0.49), residues: 304 helix: 1.64 (0.40), residues: 181 sheet: 0.45 (0.79), residues: 42 loop : 0.17 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 146 TYR 0.019 0.002 TYR F 72 PHE 0.013 0.001 PHE B 280 TRP 0.014 0.002 TRP B 287 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 2539) covalent geometry : angle 0.54508 / 0.27 ( 3418) hydrogen bonds : bond 0.02721 / 1.74 ( 119) hydrogen bonds : angle 3.71947 / 2.52 ( 330) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.5581 (OUTLIER) cc_final: 0.3186 (ptt180) REVERT: A 71 ARG cc_start: 0.7161 (mpp-170) cc_final: 0.6707 (mpp-170) REVERT: A 73 ARG cc_start: 0.8838 (tpt90) cc_final: 0.8058 (mtt180) REVERT: A 78 SER cc_start: 0.9441 (m) cc_final: 0.8966 (t) REVERT: A 83 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9161 (mm) REVERT: B 82 ASP cc_start: 0.9334 (m-30) cc_final: 0.9039 (m-30) REVERT: B 108 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 110 MET cc_start: 0.8248 (mmm) cc_final: 0.7854 (ttm) REVERT: B 174 TRP cc_start: 0.6956 (OUTLIER) cc_final: 0.3812 (t-100) REVERT: E 79 SER cc_start: 0.9321 (p) cc_final: 0.8904 (t) outliers start: 10 outliers final: 6 residues processed: 82 average time/residue: 0.0599 time to fit residues: 5.6481 Evaluate side-chains 85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 287 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 77 ASN B 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.121491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096966 restraints weight = 4656.878| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.11 r_work: 0.3152 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2539 Z= 0.123 Angle : 0.592 11.595 3418 Z= 0.287 Chirality : 0.040 0.137 389 Planarity : 0.002 0.015 432 Dihedral : 7.760 57.960 398 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.77 % Allowed : 17.36 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.49), residues: 304 helix: 1.62 (0.41), residues: 181 sheet: 0.48 (0.78), residues: 42 loop : 0.13 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 73 TYR 0.017 0.002 TYR F 72 PHE 0.014 0.001 PHE F 80 TRP 0.014 0.002 TRP B 287 HIS 0.001 0.000 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 2539) covalent geometry : angle 0.59194 / 0.29 ( 3418) hydrogen bonds : bond 0.02882 / 1.89 ( 119) hydrogen bonds : angle 3.79166 / 2.56 ( 330) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8845 (tpt90) cc_final: 0.8016 (mtt180) REVERT: A 78 SER cc_start: 0.9456 (m) cc_final: 0.8973 (t) REVERT: A 83 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9184 (mm) REVERT: B 108 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 110 MET cc_start: 0.8287 (mmm) cc_final: 0.7887 (tpt) REVERT: B 174 TRP cc_start: 0.6991 (OUTLIER) cc_final: 0.4446 (t-100) REVERT: E 79 SER cc_start: 0.9361 (p) cc_final: 0.9082 (t) REVERT: E 80 PHE cc_start: 0.7895 (t80) cc_final: 0.7660 (t80) outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.0489 time to fit residues: 4.7020 Evaluate side-chains 85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096909 restraints weight = 4676.472| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.14 r_work: 0.3137 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2539 Z= 0.118 Angle : 0.594 11.274 3418 Z= 0.284 Chirality : 0.041 0.135 389 Planarity : 0.003 0.018 432 Dihedral : 7.689 57.554 398 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.15 % Allowed : 16.23 % Favored : 79.62 % 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: 1.61 (0.49), residues: 304 helix: 1.64 (0.41), residues: 181 sheet: 0.63 (0.77), residues: 42 loop : 0.16 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 71 TYR 0.021 0.002 TYR F 72 PHE 0.012 0.001 PHE B 280 TRP 0.012 0.002 TRP B 287 HIS 0.001 0.000 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 2539) covalent geometry : angle 0.59426 / 0.28 ( 3418) hydrogen bonds : bond 0.02769 / 1.80 ( 119) hydrogen bonds : angle 3.76306 / 2.53 ( 330) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.057 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.5606 (ptt-90) cc_final: 0.3099 (ptt180) REVERT: A 73 ARG cc_start: 0.8829 (tpt90) cc_final: 0.7987 (mtt180) REVERT: A 78 SER cc_start: 0.9453 (m) cc_final: 0.8986 (t) REVERT: A 83 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9161 (mm) REVERT: B 108 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8302 (tm-30) REVERT: B 110 MET cc_start: 0.8252 (mmm) cc_final: 0.7873 (ttm) REVERT: B 174 TRP cc_start: 0.6970 (OUTLIER) cc_final: 0.4517 (t-100) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.0449 time to fit residues: 4.2472 Evaluate side-chains 82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 287 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 77 ASN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096882 restraints weight = 4688.321| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.13 r_work: 0.3145 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2539 Z= 0.125 Angle : 0.620 11.274 3418 Z= 0.302 Chirality : 0.041 0.139 389 Planarity : 0.003 0.019 432 Dihedral : 7.678 56.755 398 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.66 % Allowed : 15.09 % Favored : 79.25 % 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: 1.63 (0.50), residues: 304 helix: 1.53 (0.41), residues: 181 sheet: 0.75 (0.77), residues: 42 loop : 0.46 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 146 TYR 0.020 0.002 TYR F 72 PHE 0.018 0.002 PHE E 80 TRP 0.012 0.002 TRP B 287 HIS 0.001 0.000 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 2539) covalent geometry : angle 0.61979 / 0.30 ( 3418) hydrogen bonds : bond 0.02863 / 1.84 ( 119) hydrogen bonds : angle 3.87380 / 2.59 ( 330) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.057 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.5477 (ptt-90) cc_final: 0.3096 (ptt180) REVERT: A 73 ARG cc_start: 0.8882 (tpt90) cc_final: 0.8029 (mtt180) REVERT: A 78 SER cc_start: 0.9513 (m) cc_final: 0.9116 (t) REVERT: A 83 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9160 (mm) REVERT: B 82 ASP cc_start: 0.9306 (m-30) cc_final: 0.9051 (m-30) REVERT: B 108 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 110 MET cc_start: 0.8278 (mmm) cc_final: 0.7886 (ttm) REVERT: B 174 TRP cc_start: 0.7006 (OUTLIER) cc_final: 0.4567 (t-100) REVERT: E 80 PHE cc_start: 0.7945 (t80) cc_final: 0.7696 (t80) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.0683 time to fit residues: 6.4158 Evaluate side-chains 82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 287 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 77 ASN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.100457 restraints weight = 4736.440| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.17 r_work: 0.3250 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2539 Z= 0.123 Angle : 0.642 11.095 3418 Z= 0.311 Chirality : 0.041 0.140 389 Planarity : 0.002 0.021 432 Dihedral : 7.736 56.732 398 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.53 % Allowed : 17.36 % Favored : 78.11 % 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: 1.64 (0.50), residues: 304 helix: 1.49 (0.41), residues: 180 sheet: 0.87 (0.77), residues: 42 loop : 0.53 (0.70), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 146 TYR 0.018 0.002 TYR F 72 PHE 0.013 0.001 PHE B 80 TRP 0.011 0.002 TRP B 287 HIS 0.001 0.000 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 2539) covalent geometry : angle 0.64204 / 0.31 ( 3418) hydrogen bonds : bond 0.02813 / 1.78 ( 119) hydrogen bonds : angle 3.77529 / 2.51 ( 330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 716.92 seconds wall clock time: 12 minutes 55.39 seconds (775.39 seconds total)