Starting phenix.real_space_refine on Fri Aug 22 15:10:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vhg_43237/08_2025/8vhg_43237.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vhg_43237/08_2025/8vhg_43237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vhg_43237/08_2025/8vhg_43237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vhg_43237/08_2025/8vhg_43237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vhg_43237/08_2025/8vhg_43237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vhg_43237/08_2025/8vhg_43237.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 P 36 5.49 5 S 28 5.16 5 C 2880 2.51 5 N 844 2.21 5 O 931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4719 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2271 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 4 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1710 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain breaks: 9 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'TYR:plan': 3, 'GLN:plan1': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 0.97, per 1000 atoms: 0.21 Number of scatterers: 4719 At special positions: 0 Unit cell: (113.22, 106.08, 86.7, 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) S 28 16.00 P 36 15.00 O 931 8.00 N 844 7.00 C 2880 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: 0.32 Conformation dependent library (CDL) restraints added in 152.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 5 sheets defined 35.2% alpha, 12.7% beta 17 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 14 through 40 removed outlier: 4.048A pdb=" N LYS A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.756A pdb=" N ILE A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.835A pdb=" N SER A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 118 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.283A pdb=" N THR A 127 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.877A pdb=" N THR A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 265 removed outlier: 4.270A pdb=" N LEU A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 removed outlier: 4.447A pdb=" N GLU A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 99 removed outlier: 4.014A pdb=" N LEU B 95 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA B 96 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.904A pdb=" N LYS B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 removed outlier: 5.101A pdb=" N ARG B 153 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.532A pdb=" N LEU B 196 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 207 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.490A pdb=" N TYR B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 377 " --> pdb=" O CYS B 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 377' Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.681A pdb=" N LEU B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111 removed outlier: 7.108A pdb=" N VAL A 101 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A 111 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 99 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 98 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 198 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 195 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 168 " --> pdb=" O CYS A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 257 removed outlier: 4.071A pdb=" N SER A 246 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 339 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 337 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET A 338 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 340 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 322 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 302 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 310 removed outlier: 3.909A pdb=" N TYR A 307 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 317 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 172 removed outlier: 4.510A pdb=" N PHE B 171 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 160 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 316 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.598A pdb=" N PHE B 421 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 435 " --> pdb=" O PHE B 421 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 433 " --> pdb=" O PHE B 423 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1393 1.34 - 1.46: 1333 1.46 - 1.58: 2039 1.58 - 1.71: 69 1.71 - 1.83: 44 Bond restraints: 4878 Sorted by residual: bond pdb=" O5' DG C 12 " pdb=" C5' DG C 12 " ideal model delta sigma weight residual 1.423 1.361 0.062 3.00e-02 1.11e+03 4.24e+00 bond pdb=" P DG C 12 " pdb=" O5' DG C 12 " ideal model delta sigma weight residual 1.600 1.564 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C PRO A 334 " pdb=" O PRO A 334 " ideal model delta sigma weight residual 1.235 1.247 -0.012 7.90e-03 1.60e+04 2.18e+00 bond pdb=" C5' DG C 12 " pdb=" C4' DG C 12 " ideal model delta sigma weight residual 1.518 1.489 0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" CB ARG A 15 " pdb=" CG ARG A 15 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 ... (remaining 4873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 6534 1.80 - 3.61: 157 3.61 - 5.41: 26 5.41 - 7.21: 8 7.21 - 9.02: 2 Bond angle restraints: 6727 Sorted by residual: angle pdb=" N GLY A 97 " pdb=" CA GLY A 97 " pdb=" C GLY A 97 " ideal model delta sigma weight residual 111.21 114.85 -3.64 1.04e+00 9.25e-01 1.23e+01 angle pdb=" O5' DG C 12 " pdb=" C5' DG C 12 " pdb=" C4' DG C 12 " ideal model delta sigma weight residual 110.80 105.93 4.87 1.50e+00 4.44e-01 1.05e+01 angle pdb=" OP2 DG C 12 " pdb=" P DG C 12 " pdb=" O5' DG C 12 " ideal model delta sigma weight residual 108.00 98.98 9.02 3.00e+00 1.11e-01 9.03e+00 angle pdb=" N GLY A 266 " pdb=" CA GLY A 266 " pdb=" C GLY A 266 " ideal model delta sigma weight residual 113.18 119.29 -6.11 2.37e+00 1.78e-01 6.66e+00 angle pdb=" N LEU B 196 " pdb=" CA LEU B 196 " pdb=" CB LEU B 196 " ideal model delta sigma weight residual 111.05 107.47 3.58 1.50e+00 4.44e-01 5.69e+00 ... (remaining 6722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 2278 17.32 - 34.64: 325 34.64 - 51.96: 149 51.96 - 69.28: 52 69.28 - 86.59: 2 Dihedral angle restraints: 2806 sinusoidal: 1307 harmonic: 1499 Sorted by residual: dihedral pdb=" CA THR B 401 " pdb=" C THR B 401 " pdb=" N ASN B 402 " pdb=" CA ASN B 402 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN B 402 " pdb=" C ASN B 402 " pdb=" N CYS B 403 " pdb=" CA CYS B 403 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA SER B 418 " pdb=" C SER B 418 " pdb=" N ARG B 419 " pdb=" CA ARG B 419 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 489 0.035 - 0.069: 197 0.069 - 0.104: 60 0.104 - 0.139: 21 0.139 - 0.174: 3 Chirality restraints: 770 Sorted by residual: chirality pdb=" CG LEU A 222 " pdb=" CB LEU A 222 " pdb=" CD1 LEU A 222 " pdb=" CD2 LEU A 222 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA VAL A 199 " pdb=" N VAL A 199 " pdb=" C VAL A 199 " pdb=" CB VAL A 199 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CB VAL A 199 " pdb=" CA VAL A 199 " pdb=" CG1 VAL A 199 " pdb=" CG2 VAL A 199 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 767 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 425 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO B 426 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 426 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 426 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 24 " -0.168 9.50e-02 1.11e+02 7.52e-02 3.52e+00 pdb=" NE ARG A 24 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 24 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 24 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 24 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 268 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A 269 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.026 5.00e-02 4.00e+02 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1274 2.82 - 3.34: 4296 3.34 - 3.86: 7422 3.86 - 4.38: 8100 4.38 - 4.90: 12698 Nonbonded interactions: 33790 Sorted by model distance: nonbonded pdb=" O5' DG C 12 " pdb=" O4' DG C 12 " model vdw 2.303 2.432 nonbonded pdb=" O5' DC D 4 " pdb=" O4' DC D 4 " model vdw 2.502 2.432 nonbonded pdb=" O5' DG C 3 " pdb=" O4' DG C 3 " model vdw 2.511 2.432 nonbonded pdb=" O5' DT C 13 " pdb=" O4' DT C 13 " model vdw 2.538 2.432 nonbonded pdb=" O5' DG C 16 " pdb=" O4' DG C 16 " model vdw 2.546 2.432 ... (remaining 33785 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 2.180 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.770 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: 9.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 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 0.062 4878 Z= 0.204 Angle : 0.727 9.017 6727 Z= 0.398 Chirality : 0.043 0.174 770 Planarity : 0.007 0.075 720 Dihedral : 20.382 86.594 1820 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.66 % Allowed : 4.12 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.37), residues: 482 helix: -0.58 (0.43), residues: 140 sheet: -2.41 (0.47), residues: 99 loop : -2.45 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 15 TYR 0.016 0.002 TYR B 287 PHE 0.014 0.002 PHE B 171 TRP 0.006 0.001 TRP A 318 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 4878) covalent geometry : angle 0.72679 ( 6727) hydrogen bonds : bond 0.17228 ( 173) hydrogen bonds : angle 7.31331 ( 449) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.6727 (m) cc_final: 0.6490 (t) REVERT: A 191 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.6220 (mttt) REVERT: A 256 TYR cc_start: 0.6646 (t80) cc_final: 0.5887 (t80) REVERT: A 273 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6249 (mm) REVERT: A 287 GLU cc_start: 0.8028 (pp20) cc_final: 0.7628 (pp20) REVERT: B 91 PHE cc_start: 0.6909 (m-80) cc_final: 0.6509 (m-10) REVERT: B 184 GLN cc_start: 0.7629 (mm-40) cc_final: 0.6451 (pt0) REVERT: B 338 MET cc_start: 0.7024 (tpp) cc_final: 0.6601 (mmm) outliers start: 11 outliers final: 6 residues processed: 125 average time/residue: 0.0809 time to fit residues: 12.1015 Evaluate side-chains 118 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 343 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.112320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.103336 restraints weight = 16470.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.105130 restraints weight = 9772.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.106326 restraints weight = 6349.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.107155 restraints weight = 4425.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.107750 restraints weight = 3267.162| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4878 Z= 0.170 Angle : 0.640 6.419 6727 Z= 0.351 Chirality : 0.041 0.133 770 Planarity : 0.004 0.039 720 Dihedral : 22.020 82.784 939 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.84 % Allowed : 12.83 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.38), residues: 482 helix: -0.35 (0.42), residues: 146 sheet: -2.36 (0.49), residues: 100 loop : -2.28 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 83 TYR 0.008 0.001 TYR A 307 PHE 0.015 0.002 PHE A 244 TRP 0.007 0.002 TRP A 318 HIS 0.011 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4878) covalent geometry : angle 0.63991 ( 6727) hydrogen bonds : bond 0.05960 ( 173) hydrogen bonds : angle 5.51070 ( 449) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7261 (pp) REVERT: A 140 HIS cc_start: 0.6065 (OUTLIER) cc_final: 0.5720 (p90) REVERT: A 191 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.6233 (mttt) REVERT: A 256 TYR cc_start: 0.6319 (t80) cc_final: 0.5701 (t80) REVERT: A 273 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5789 (mm) REVERT: A 287 GLU cc_start: 0.7971 (pp20) cc_final: 0.7570 (pp20) REVERT: B 87 LYS cc_start: 0.8003 (mmmm) cc_final: 0.6994 (pttm) REVERT: B 184 GLN cc_start: 0.7628 (mm-40) cc_final: 0.6526 (pt0) REVERT: B 338 MET cc_start: 0.6934 (tpp) cc_final: 0.6530 (mmm) outliers start: 20 outliers final: 10 residues processed: 121 average time/residue: 0.0956 time to fit residues: 13.7643 Evaluate side-chains 121 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.0370 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.6860 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.111760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.102896 restraints weight = 16673.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.104692 restraints weight = 9793.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.105883 restraints weight = 6322.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.106707 restraints weight = 4385.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.107271 restraints weight = 3220.276| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4878 Z= 0.178 Angle : 0.637 5.544 6727 Z= 0.351 Chirality : 0.041 0.128 770 Planarity : 0.004 0.041 720 Dihedral : 21.813 72.822 935 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 5.08 % Allowed : 18.16 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.38), residues: 482 helix: -0.13 (0.43), residues: 146 sheet: -1.98 (0.49), residues: 104 loop : -2.50 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 83 TYR 0.010 0.001 TYR A 307 PHE 0.024 0.002 PHE A 110 TRP 0.009 0.002 TRP A 318 HIS 0.008 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 4878) covalent geometry : angle 0.63741 ( 6727) hydrogen bonds : bond 0.05680 ( 173) hydrogen bonds : angle 5.23600 ( 449) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6917 (pp) REVERT: A 140 HIS cc_start: 0.6217 (OUTLIER) cc_final: 0.5985 (p90) REVERT: A 191 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6233 (mttt) REVERT: A 273 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5782 (mm) REVERT: A 287 GLU cc_start: 0.7970 (pp20) cc_final: 0.7641 (pp20) REVERT: B 87 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7171 (pttm) REVERT: B 184 GLN cc_start: 0.7775 (mm-40) cc_final: 0.6691 (pt0) REVERT: B 338 MET cc_start: 0.6912 (tpp) cc_final: 0.6511 (mmm) outliers start: 21 outliers final: 15 residues processed: 114 average time/residue: 0.0938 time to fit residues: 12.7748 Evaluate side-chains 122 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 0.0000 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.112814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.103483 restraints weight = 16759.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.105379 restraints weight = 9850.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.106654 restraints weight = 6355.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.107546 restraints weight = 4400.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.108181 restraints weight = 3224.438| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4878 Z= 0.139 Angle : 0.588 5.505 6727 Z= 0.322 Chirality : 0.039 0.130 770 Planarity : 0.004 0.036 720 Dihedral : 21.713 69.111 935 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.60 % Allowed : 22.03 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.38), residues: 482 helix: 0.10 (0.44), residues: 146 sheet: -1.92 (0.51), residues: 98 loop : -2.25 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 250 TYR 0.008 0.001 TYR A 35 PHE 0.011 0.001 PHE B 171 TRP 0.006 0.001 TRP A 318 HIS 0.006 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4878) covalent geometry : angle 0.58844 ( 6727) hydrogen bonds : bond 0.04771 ( 173) hydrogen bonds : angle 4.83926 ( 449) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6837 (pp) REVERT: A 191 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6289 (mttt) REVERT: A 287 GLU cc_start: 0.7979 (pp20) cc_final: 0.7712 (pp20) REVERT: B 87 LYS cc_start: 0.7790 (mmmm) cc_final: 0.7120 (pttm) REVERT: B 184 GLN cc_start: 0.7749 (mm-40) cc_final: 0.6607 (pt0) REVERT: B 338 MET cc_start: 0.6893 (tpp) cc_final: 0.6451 (mmm) outliers start: 19 outliers final: 12 residues processed: 114 average time/residue: 0.0958 time to fit residues: 13.0688 Evaluate side-chains 114 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 361 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 0.0020 chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.2926 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.113396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.104195 restraints weight = 16851.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.106075 restraints weight = 9911.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.107350 restraints weight = 6405.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.108249 restraints weight = 4432.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.108842 restraints weight = 3235.342| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4878 Z= 0.125 Angle : 0.565 5.483 6727 Z= 0.310 Chirality : 0.038 0.126 770 Planarity : 0.004 0.039 720 Dihedral : 21.581 66.457 933 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.84 % Allowed : 22.52 % Favored : 72.64 % 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 aren not related in a simple way. whole: -2.07 (0.39), residues: 482 helix: 0.02 (0.43), residues: 153 sheet: -1.78 (0.51), residues: 100 loop : -2.15 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 83 TYR 0.006 0.001 TYR A 307 PHE 0.021 0.001 PHE A 110 TRP 0.003 0.001 TRP A 318 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4878) covalent geometry : angle 0.56528 ( 6727) hydrogen bonds : bond 0.04090 ( 173) hydrogen bonds : angle 4.53779 ( 449) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6199 (pp) REVERT: A 191 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6332 (mttt) REVERT: A 287 GLU cc_start: 0.7972 (pp20) cc_final: 0.7737 (pp20) REVERT: B 83 ARG cc_start: 0.7257 (mtm110) cc_final: 0.6994 (mtm110) REVERT: B 87 LYS cc_start: 0.7760 (mmmm) cc_final: 0.7154 (pttm) REVERT: B 184 GLN cc_start: 0.7778 (mm-40) cc_final: 0.6636 (pt0) REVERT: B 338 MET cc_start: 0.6874 (tpp) cc_final: 0.6458 (mmm) outliers start: 20 outliers final: 14 residues processed: 116 average time/residue: 0.0888 time to fit residues: 12.4377 Evaluate side-chains 117 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 361 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.111509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.102088 restraints weight = 16922.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.104034 restraints weight = 9742.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.105330 restraints weight = 6215.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.106211 restraints weight = 4277.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.106860 restraints weight = 3125.711| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4878 Z= 0.169 Angle : 0.622 5.901 6727 Z= 0.341 Chirality : 0.040 0.130 770 Planarity : 0.004 0.040 720 Dihedral : 21.539 68.390 933 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 6.30 % Allowed : 21.79 % Favored : 71.91 % 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 aren not related in a simple way. whole: -2.06 (0.39), residues: 482 helix: 0.19 (0.44), residues: 147 sheet: -1.75 (0.52), residues: 99 loop : -2.23 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 83 TYR 0.009 0.001 TYR A 307 PHE 0.013 0.002 PHE A 244 TRP 0.008 0.002 TRP A 318 HIS 0.005 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4878) covalent geometry : angle 0.62228 ( 6727) hydrogen bonds : bond 0.04995 ( 173) hydrogen bonds : angle 4.82066 ( 449) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6264 (pp) REVERT: A 191 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6343 (mttt) REVERT: A 287 GLU cc_start: 0.7968 (pp20) cc_final: 0.7746 (pp20) REVERT: B 87 LYS cc_start: 0.7819 (mmmm) cc_final: 0.7401 (mppt) REVERT: B 184 GLN cc_start: 0.7828 (mm-40) cc_final: 0.6814 (pt0) REVERT: B 338 MET cc_start: 0.6879 (tpp) cc_final: 0.6466 (mmm) outliers start: 26 outliers final: 20 residues processed: 114 average time/residue: 0.0865 time to fit residues: 11.8433 Evaluate side-chains 123 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 9 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.112647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.103318 restraints weight = 16432.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105247 restraints weight = 9470.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.106557 restraints weight = 6032.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.107464 restraints weight = 4126.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.108103 restraints weight = 2999.734| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4878 Z= 0.140 Angle : 0.603 6.831 6727 Z= 0.328 Chirality : 0.039 0.128 770 Planarity : 0.004 0.040 720 Dihedral : 21.527 67.132 933 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.81 % Allowed : 23.24 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.39), residues: 482 helix: 0.05 (0.44), residues: 153 sheet: -1.69 (0.53), residues: 98 loop : -2.18 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 83 TYR 0.011 0.001 TYR B 340 PHE 0.012 0.001 PHE A 244 TRP 0.005 0.001 TRP A 318 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4878) covalent geometry : angle 0.60313 ( 6727) hydrogen bonds : bond 0.04438 ( 173) hydrogen bonds : angle 4.65712 ( 449) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6086 (pp) REVERT: A 191 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6359 (mttt) REVERT: A 287 GLU cc_start: 0.7989 (pp20) cc_final: 0.7594 (pp20) REVERT: B 87 LYS cc_start: 0.7769 (mmmm) cc_final: 0.7201 (pttm) REVERT: B 184 GLN cc_start: 0.7804 (mm-40) cc_final: 0.6739 (pt0) REVERT: B 406 PHE cc_start: 0.3752 (OUTLIER) cc_final: 0.3483 (t80) outliers start: 24 outliers final: 18 residues processed: 113 average time/residue: 0.0904 time to fit residues: 12.2425 Evaluate side-chains 119 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 406 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.0670 chunk 36 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.111551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.102591 restraints weight = 16867.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.104445 restraints weight = 9706.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.105680 restraints weight = 6172.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.106549 restraints weight = 4234.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.107142 restraints weight = 3071.338| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4878 Z= 0.171 Angle : 0.652 8.035 6727 Z= 0.353 Chirality : 0.040 0.131 770 Planarity : 0.004 0.044 720 Dihedral : 21.532 67.364 929 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 6.05 % Allowed : 22.28 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.39), residues: 482 helix: 0.23 (0.45), residues: 147 sheet: -1.72 (0.52), residues: 100 loop : -2.22 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 319 TYR 0.010 0.001 TYR B 195 PHE 0.011 0.002 PHE A 110 TRP 0.008 0.002 TRP A 318 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4878) covalent geometry : angle 0.65202 ( 6727) hydrogen bonds : bond 0.04990 ( 173) hydrogen bonds : angle 4.80320 ( 449) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6199 (pp) REVERT: A 191 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6386 (mttt) REVERT: A 287 GLU cc_start: 0.8009 (pp20) cc_final: 0.7626 (pp20) REVERT: B 83 ARG cc_start: 0.7396 (mtm110) cc_final: 0.7188 (mtm110) REVERT: B 87 LYS cc_start: 0.7776 (mmmm) cc_final: 0.7131 (pttm) REVERT: B 184 GLN cc_start: 0.7801 (mm-40) cc_final: 0.6798 (pt0) REVERT: B 338 MET cc_start: 0.6863 (tpp) cc_final: 0.6467 (mmm) REVERT: B 406 PHE cc_start: 0.3857 (OUTLIER) cc_final: 0.3555 (t80) outliers start: 25 outliers final: 19 residues processed: 114 average time/residue: 0.0980 time to fit residues: 13.4113 Evaluate side-chains 124 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.111571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.102408 restraints weight = 16593.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104345 restraints weight = 9431.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.105620 restraints weight = 5959.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.106536 restraints weight = 4066.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.107157 restraints weight = 2921.724| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4878 Z= 0.168 Angle : 0.655 8.324 6727 Z= 0.354 Chirality : 0.040 0.149 770 Planarity : 0.004 0.042 720 Dihedral : 21.559 65.815 929 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 5.57 % Allowed : 24.21 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.39), residues: 482 helix: 0.17 (0.45), residues: 147 sheet: -1.70 (0.52), residues: 100 loop : -2.25 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 343 TYR 0.010 0.001 TYR B 195 PHE 0.013 0.002 PHE A 110 TRP 0.008 0.002 TRP A 318 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 4878) covalent geometry : angle 0.65475 ( 6727) hydrogen bonds : bond 0.04950 ( 173) hydrogen bonds : angle 4.71073 ( 449) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6168 (pp) REVERT: A 191 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6427 (mttt) REVERT: B 87 LYS cc_start: 0.7781 (mmmm) cc_final: 0.7160 (pttm) REVERT: B 112 LEU cc_start: 0.7880 (mm) cc_final: 0.7623 (mp) REVERT: B 184 GLN cc_start: 0.7821 (mm-40) cc_final: 0.6784 (pt0) REVERT: B 338 MET cc_start: 0.6895 (tpp) cc_final: 0.6491 (mmm) REVERT: B 406 PHE cc_start: 0.3898 (OUTLIER) cc_final: 0.3586 (t80) outliers start: 23 outliers final: 19 residues processed: 116 average time/residue: 0.0873 time to fit residues: 12.1657 Evaluate side-chains 124 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 0.3980 chunk 49 optimal weight: 0.0030 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.1222 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.114639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.105933 restraints weight = 16836.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.107754 restraints weight = 9814.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.108973 restraints weight = 6301.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.109801 restraints weight = 4348.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.110398 restraints weight = 3171.460| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4878 Z= 0.120 Angle : 0.607 7.573 6727 Z= 0.323 Chirality : 0.038 0.125 770 Planarity : 0.004 0.041 720 Dihedral : 21.494 61.198 929 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.84 % Allowed : 24.94 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.38), residues: 482 helix: 0.15 (0.43), residues: 153 sheet: -1.54 (0.52), residues: 101 loop : -2.03 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 84 TYR 0.011 0.001 TYR B 340 PHE 0.010 0.001 PHE A 244 TRP 0.003 0.001 TRP A 190 HIS 0.004 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4878) covalent geometry : angle 0.60689 ( 6727) hydrogen bonds : bond 0.03407 ( 173) hydrogen bonds : angle 4.28514 ( 449) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.5743 (pp) REVERT: A 191 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6519 (mttt) REVERT: A 287 GLU cc_start: 0.8011 (pp20) cc_final: 0.7586 (pp20) REVERT: B 87 LYS cc_start: 0.7637 (mmmm) cc_final: 0.7037 (pttm) REVERT: B 112 LEU cc_start: 0.7791 (mm) cc_final: 0.7582 (mp) REVERT: B 184 GLN cc_start: 0.7767 (mm-40) cc_final: 0.6616 (pt0) REVERT: B 314 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7350 (tt) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.0763 time to fit residues: 11.0858 Evaluate side-chains 124 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.113457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.104499 restraints weight = 17080.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.106368 restraints weight = 9895.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.107631 restraints weight = 6339.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.108499 restraints weight = 4365.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.109119 restraints weight = 3186.500| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4878 Z= 0.134 Angle : 0.628 10.647 6727 Z= 0.334 Chirality : 0.040 0.168 770 Planarity : 0.004 0.039 720 Dihedral : 21.363 60.827 929 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.84 % Allowed : 26.39 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.38), residues: 482 helix: 0.19 (0.44), residues: 153 sheet: -1.33 (0.51), residues: 103 loop : -2.06 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.011 0.001 TYR B 340 PHE 0.011 0.001 PHE A 244 TRP 0.009 0.001 TRP A 190 HIS 0.005 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4878) covalent geometry : angle 0.62781 ( 6727) hydrogen bonds : bond 0.03916 ( 173) hydrogen bonds : angle 4.27652 ( 449) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 994.37 seconds wall clock time: 17 minutes 44.61 seconds (1064.61 seconds total)