Starting phenix.real_space_refine on Wed Sep 17 08:33:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d85_46630/09_2025/9d85_46630_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d85_46630/09_2025/9d85_46630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d85_46630/09_2025/9d85_46630_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d85_46630/09_2025/9d85_46630_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d85_46630/09_2025/9d85_46630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d85_46630/09_2025/9d85_46630.map" } resolution = 3.59 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= 0.045 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 65 5.49 5 S 27 5.16 5 C 4342 2.51 5 N 1229 2.21 5 O 1538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7201 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1585 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 188} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1114 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "K" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2502 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 310} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "P" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 615 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "T" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1385 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 11, 'rna3p_pur': 28, 'rna3p_pyr': 23} Link IDs: {'rna2p': 14, 'rna3p': 50} Chain breaks: 3 Time building chain proxies: 1.96, per 1000 atoms: 0.27 Number of scatterers: 7201 At special positions: 0 Unit cell: (70.04, 89.61, 130.81, 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 27 16.00 P 65 15.00 O 1538 8.00 N 1229 7.00 C 4342 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 Atom "ATOM 5823 O4' G T 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 324.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 53.5% alpha, 14.7% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'B' and resid 369 through 391 Processing helix chain 'B' and resid 392 through 395 Processing helix chain 'B' and resid 421 through 426 removed outlier: 4.443A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.817A pdb=" N TYR B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 496 removed outlier: 3.771A pdb=" N LYS B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 Processing helix chain 'B' and resid 516 through 529 removed outlier: 3.964A pdb=" N ILE B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 4.125A pdb=" N ASN C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 51 Processing helix chain 'C' and resid 57 through 68 removed outlier: 4.094A pdb=" N LEU C 63 " --> pdb=" O TRP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 removed outlier: 3.598A pdb=" N ALA C 75 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 104 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 115 through 124 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'K' and resid 45 through 63 Proline residue: K 53 - end of helix Processing helix chain 'K' and resid 79 through 98 Processing helix chain 'K' and resid 106 through 118 removed outlier: 3.747A pdb=" N ILE K 111 " --> pdb=" O CYS K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 166 Processing helix chain 'K' and resid 170 through 179 removed outlier: 4.339A pdb=" N TYR K 174 " --> pdb=" O PRO K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 212 Processing helix chain 'K' and resid 215 through 243 Processing helix chain 'K' and resid 251 through 255 Processing helix chain 'K' and resid 256 through 270 removed outlier: 3.961A pdb=" N ARG K 260 " --> pdb=" O ASN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.623A pdb=" N GLY K 283 " --> pdb=" O LYS K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 299 removed outlier: 4.250A pdb=" N ILE K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN K 299 " --> pdb=" O LEU K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 Processing helix chain 'K' and resid 315 through 319 removed outlier: 3.571A pdb=" N VAL K 319 " --> pdb=" O THR K 316 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 32 removed outlier: 4.095A pdb=" N TYR P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 80 removed outlier: 3.833A pdb=" N ILE P 80 " --> pdb=" O ALA P 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 346 through 351 Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AA3, first strand: chain 'B' and resid 447 through 449 Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA5, first strand: chain 'K' and resid 23 through 31 removed outlier: 3.525A pdb=" N GLU K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE K 17 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN K 27 " --> pdb=" O VAL K 15 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL K 15 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR K 29 " --> pdb=" O THR K 13 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR K 13 " --> pdb=" O THR K 29 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE K 71 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL K 104 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE K 73 " --> pdb=" O VAL K 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 143 through 148 removed outlier: 6.527A pdb=" N VAL K 135 " --> pdb=" O PHE K 146 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU K 148 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR K 133 " --> pdb=" O GLU K 148 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU K 124 " --> pdb=" O MET K 248 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL K 250 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU K 126 " --> pdb=" O VAL K 250 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 247 " --> pdb=" O ASP K 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 192 through 193 removed outlier: 3.669A pdb=" N LYS K 193 " --> pdb=" O ASP K 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 7 through 13 324 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1430 1.33 - 1.45: 1919 1.45 - 1.57: 3937 1.57 - 1.69: 126 1.69 - 1.81: 46 Bond restraints: 7458 Sorted by residual: bond pdb=" CA PRO K 34 " pdb=" C PRO K 34 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.21e+01 bond pdb=" N GLN K 37 " pdb=" CA GLN K 37 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.27e-02 6.20e+03 1.03e+01 bond pdb=" C LYS K 33 " pdb=" N PRO K 34 " ideal model delta sigma weight residual 1.329 1.365 -0.036 1.18e-02 7.18e+03 9.17e+00 bond pdb=" N LYS K 33 " pdb=" CA LYS K 33 " ideal model delta sigma weight residual 1.457 1.498 -0.042 1.41e-02 5.03e+03 8.70e+00 bond pdb=" O5' U T 44 " pdb=" C5' U T 44 " ideal model delta sigma weight residual 1.420 1.464 -0.044 1.50e-02 4.44e+03 8.63e+00 ... (remaining 7453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.23: 10335 6.23 - 12.46: 34 12.46 - 18.69: 8 18.69 - 24.92: 3 24.92 - 31.15: 3 Bond angle restraints: 10383 Sorted by residual: angle pdb=" N TYR K 32 " pdb=" CA TYR K 32 " pdb=" C TYR K 32 " ideal model delta sigma weight residual 109.96 78.81 31.15 1.50e+00 4.44e-01 4.31e+02 angle pdb=" C ARG B 529 " pdb=" CA ARG B 529 " pdb=" CB ARG B 529 " ideal model delta sigma weight residual 110.94 81.56 29.38 1.65e+00 3.67e-01 3.17e+02 angle pdb=" N LYS K 33 " pdb=" CA LYS K 33 " pdb=" CB LYS K 33 " ideal model delta sigma weight residual 110.37 83.48 26.89 1.78e+00 3.16e-01 2.28e+02 angle pdb=" N ARG B 529 " pdb=" CA ARG B 529 " pdb=" C ARG B 529 " ideal model delta sigma weight residual 112.72 128.78 -16.06 1.14e+00 7.69e-01 1.98e+02 angle pdb=" N GLU K 43 " pdb=" CA GLU K 43 " pdb=" C GLU K 43 " ideal model delta sigma weight residual 110.33 93.31 17.02 1.29e+00 6.01e-01 1.74e+02 ... (remaining 10378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.86: 4306 33.86 - 67.71: 277 67.71 - 101.57: 40 101.57 - 135.43: 3 135.43 - 169.28: 3 Dihedral angle restraints: 4629 sinusoidal: 2487 harmonic: 2142 Sorted by residual: dihedral pdb=" C ARG B 529 " pdb=" N ARG B 529 " pdb=" CA ARG B 529 " pdb=" CB ARG B 529 " ideal model delta harmonic sigma weight residual -122.60 -94.98 -27.62 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" N LYS K 33 " pdb=" C LYS K 33 " pdb=" CA LYS K 33 " pdb=" CB LYS K 33 " ideal model delta harmonic sigma weight residual 122.80 96.34 26.46 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" C TYR K 32 " pdb=" N TYR K 32 " pdb=" CA TYR K 32 " pdb=" CB TYR K 32 " ideal model delta harmonic sigma weight residual -122.60 -97.19 -25.41 0 2.50e+00 1.60e-01 1.03e+02 ... (remaining 4626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1168 0.125 - 0.249: 45 0.249 - 0.374: 2 0.374 - 0.499: 14 0.499 - 0.623: 9 Chirality restraints: 1238 Sorted by residual: chirality pdb=" CA TYR K 32 " pdb=" N TYR K 32 " pdb=" C TYR K 32 " pdb=" CB TYR K 32 " both_signs ideal model delta sigma weight residual False 2.51 3.13 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" P U T 44 " pdb=" OP1 U T 44 " pdb=" OP2 U T 44 " pdb=" O5' U T 44 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" P C T 40 " pdb=" OP1 C T 40 " pdb=" OP2 C T 40 " pdb=" O5' C T 40 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.00e+00 ... (remaining 1235 not shown) Planarity restraints: 1083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 532 " -1.008 9.50e-02 1.11e+02 4.52e-01 1.23e+02 pdb=" NE ARG B 532 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 532 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 532 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 532 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 163 " -0.809 9.50e-02 1.11e+02 3.63e-01 8.01e+01 pdb=" NE ARG K 163 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG K 163 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG K 163 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 163 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 526 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.64e+00 pdb=" C ASP B 526 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP B 526 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 527 " 0.018 2.00e-02 2.50e+03 ... (remaining 1080 not shown) Histogram of nonbonded interaction distances: 0.99 - 1.77: 7 1.77 - 2.56: 162 2.56 - 3.34: 10118 3.34 - 4.12: 19580 4.12 - 4.90: 32785 Warning: very small nonbonded interaction distances. Nonbonded interactions: 62652 Sorted by model distance: nonbonded pdb=" CE1 HIS C 73 " pdb=" O4' G T 1 " model vdw 0.994 3.260 nonbonded pdb=" CE1 PHE C 21 " pdb=" N7 A T 76 " model vdw 1.188 3.420 nonbonded pdb=" CZ PHE C 21 " pdb=" C5 A T 76 " model vdw 1.329 3.560 nonbonded pdb=" CE1 PHE C 21 " pdb=" C5 A T 76 " model vdw 1.449 3.560 nonbonded pdb=" CD1 PHE C 21 " pdb=" N7 A T 76 " model vdw 1.565 3.420 ... (remaining 62647 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=0.50 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: 1.420 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4417 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 : 0.005 0.050 7458 Z= 0.313 Angle : 1.213 31.151 10383 Z= 0.765 Chirality : 0.083 0.623 1238 Planarity : 0.018 0.452 1083 Dihedral : 21.010 169.283 3249 Min Nonbonded Distance : 0.994 Molprobity Statistics. All-atom Clashscore : 27.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.43 % Favored : 93.43 % Rotamer: Outliers : 0.33 % Allowed : 0.33 % Favored : 99.35 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 9.09 % 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: -1.10 (0.31), residues: 731 helix: 0.13 (0.27), residues: 348 sheet: -0.51 (0.57), residues: 95 loop : -1.83 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 163 TYR 0.019 0.002 TYR K 226 PHE 0.011 0.001 PHE B 506 TRP 0.027 0.002 TRP P 72 HIS 0.002 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 7458) covalent geometry : angle 1.21268 (10383) hydrogen bonds : bond 0.15986 ( 357) hydrogen bonds : angle 6.88297 ( 964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.4362 (mtm) cc_final: 0.3609 (mtm) REVERT: B 470 LEU cc_start: 0.6470 (mp) cc_final: 0.5907 (tt) REVERT: C 60 MET cc_start: 0.5579 (tmm) cc_final: 0.4329 (mtm) REVERT: C 70 ARG cc_start: 0.5801 (mtt-85) cc_final: 0.5424 (tpt170) REVERT: C 115 ASN cc_start: 0.8670 (p0) cc_final: 0.7844 (p0) REVERT: C 116 GLU cc_start: 0.8302 (pp20) cc_final: 0.8003 (pm20) REVERT: K 204 THR cc_start: 0.8004 (m) cc_final: 0.7645 (p) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.1109 time to fit residues: 23.0668 Evaluate side-chains 99 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN C 22 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.180061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.155751 restraints weight = 21298.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.159797 restraints weight = 12063.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.162584 restraints weight = 8044.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.164443 restraints weight = 5998.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.165767 restraints weight = 4808.017| |-----------------------------------------------------------------------------| r_work (final): 0.4865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4865 r_free = 0.4865 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4864 r_free = 0.4864 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4838 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7458 Z= 0.184 Angle : 0.775 8.098 10383 Z= 0.404 Chirality : 0.047 0.198 1238 Planarity : 0.005 0.055 1083 Dihedral : 22.985 167.575 1841 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.11 % Allowed : 14.63 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.94 (0.30), residues: 731 helix: 0.17 (0.27), residues: 356 sheet: -0.76 (0.53), residues: 99 loop : -1.53 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 368 TYR 0.023 0.003 TYR B 510 PHE 0.025 0.003 PHE K 281 TRP 0.018 0.003 TRP K 291 HIS 0.013 0.003 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7458) covalent geometry : angle 0.77458 (10383) hydrogen bonds : bond 0.05929 ( 357) hydrogen bonds : angle 5.50423 ( 964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.4572 (tptp) cc_final: 0.4096 (tptm) REVERT: B 470 LEU cc_start: 0.6185 (mp) cc_final: 0.5914 (tt) REVERT: C 60 MET cc_start: 0.5272 (tmm) cc_final: 0.4844 (ptp) REVERT: C 70 ARG cc_start: 0.5896 (mtt-85) cc_final: 0.5099 (tpt170) REVERT: C 115 ASN cc_start: 0.8403 (p0) cc_final: 0.8161 (p0) REVERT: C 124 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6941 (pm20) outliers start: 13 outliers final: 6 residues processed: 128 average time/residue: 0.0858 time to fit residues: 14.2372 Evaluate side-chains 97 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN B 495 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.170248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.143641 restraints weight = 21521.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.147869 restraints weight = 12146.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.150608 restraints weight = 8270.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.152537 restraints weight = 6354.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.153540 restraints weight = 5264.819| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 7458 Z= 0.308 Angle : 0.949 13.261 10383 Z= 0.486 Chirality : 0.053 0.338 1238 Planarity : 0.006 0.060 1083 Dihedral : 22.902 165.663 1841 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.04 % Allowed : 20.65 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.81 (0.29), residues: 731 helix: -0.60 (0.25), residues: 349 sheet: -1.31 (0.49), residues: 109 loop : -1.77 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 84 TYR 0.031 0.003 TYR K 190 PHE 0.027 0.004 PHE K 146 TRP 0.033 0.004 TRP K 291 HIS 0.014 0.003 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 7458) covalent geometry : angle 0.94938 (10383) hydrogen bonds : bond 0.08088 ( 357) hydrogen bonds : angle 6.16551 ( 964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.5267 (tptp) cc_final: 0.4879 (tmtt) REVERT: C 115 ASN cc_start: 0.8711 (p0) cc_final: 0.8352 (p0) REVERT: C 119 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7582 (mm-30) REVERT: C 121 LEU cc_start: 0.7907 (pp) cc_final: 0.7569 (pp) REVERT: K 248 MET cc_start: 0.4145 (tpp) cc_final: 0.3836 (tpp) REVERT: K 261 GLU cc_start: 0.6670 (mp0) cc_final: 0.6462 (mm-30) REVERT: K 266 MET cc_start: 0.1708 (tmm) cc_final: -0.0347 (ttt) outliers start: 31 outliers final: 19 residues processed: 144 average time/residue: 0.0885 time to fit residues: 17.0823 Evaluate side-chains 109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 289 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 HIS ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.173320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.147662 restraints weight = 21495.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.151951 restraints weight = 11994.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.154790 restraints weight = 8042.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.156558 restraints weight = 6066.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.157822 restraints weight = 4985.836| |-----------------------------------------------------------------------------| r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.7551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7458 Z= 0.163 Angle : 0.748 11.280 10383 Z= 0.379 Chirality : 0.045 0.197 1238 Planarity : 0.004 0.037 1083 Dihedral : 22.458 168.608 1841 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.07 % Allowed : 23.58 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.32 (0.29), residues: 731 helix: -0.28 (0.26), residues: 353 sheet: -1.12 (0.48), residues: 110 loop : -1.39 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 84 TYR 0.023 0.002 TYR B 415 PHE 0.020 0.003 PHE P 14 TRP 0.026 0.002 TRP K 291 HIS 0.009 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7458) covalent geometry : angle 0.74821 (10383) hydrogen bonds : bond 0.05743 ( 357) hydrogen bonds : angle 5.44581 ( 964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ASP cc_start: 0.7675 (t70) cc_final: 0.7407 (t0) REVERT: C 115 ASN cc_start: 0.8754 (p0) cc_final: 0.8361 (p0) REVERT: C 117 ASP cc_start: 0.8046 (m-30) cc_final: 0.7554 (m-30) REVERT: C 119 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7574 (mm-30) REVERT: K 248 MET cc_start: 0.4324 (tpp) cc_final: 0.3960 (tpp) REVERT: K 261 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6284 (mm-30) REVERT: K 266 MET cc_start: 0.1590 (tmm) cc_final: -0.0246 (ttt) REVERT: K 288 MET cc_start: 0.4747 (ppp) cc_final: 0.4477 (ppp) outliers start: 25 outliers final: 13 residues processed: 130 average time/residue: 0.0713 time to fit residues: 13.0251 Evaluate side-chains 109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.170927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.144536 restraints weight = 21145.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.148750 restraints weight = 12042.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.151428 restraints weight = 8214.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.153378 restraints weight = 6304.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.154734 restraints weight = 5170.915| |-----------------------------------------------------------------------------| r_work (final): 0.4768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.8269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7458 Z= 0.173 Angle : 0.754 11.818 10383 Z= 0.373 Chirality : 0.044 0.166 1238 Planarity : 0.004 0.041 1083 Dihedral : 22.279 167.772 1841 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.88 % Allowed : 26.02 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.14 (0.30), residues: 731 helix: -0.14 (0.26), residues: 351 sheet: -1.00 (0.47), residues: 119 loop : -1.28 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 84 TYR 0.019 0.002 TYR K 190 PHE 0.017 0.002 PHE P 14 TRP 0.022 0.003 TRP B 503 HIS 0.008 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 7458) covalent geometry : angle 0.75446 (10383) hydrogen bonds : bond 0.05927 ( 357) hydrogen bonds : angle 5.41044 ( 964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.4436 (OUTLIER) cc_final: 0.4070 (ptm) REVERT: C 60 MET cc_start: 0.4855 (tmm) cc_final: 0.4183 (mtt) REVERT: C 115 ASN cc_start: 0.8770 (p0) cc_final: 0.8323 (p0) REVERT: K 164 TYR cc_start: 0.4539 (m-80) cc_final: 0.4055 (m-80) REVERT: K 248 MET cc_start: 0.4188 (tpp) cc_final: 0.3831 (tpp) REVERT: K 266 MET cc_start: 0.1854 (tmm) cc_final: 0.0278 (ttt) REVERT: K 288 MET cc_start: 0.4530 (ppp) cc_final: 0.3621 (ppp) outliers start: 30 outliers final: 19 residues processed: 123 average time/residue: 0.0792 time to fit residues: 13.4915 Evaluate side-chains 112 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 291 TRP Chi-restraints excluded: chain K residue 311 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.164643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.137309 restraints weight = 20841.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.141229 restraints weight = 12172.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.143845 restraints weight = 8505.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.145606 restraints weight = 6648.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.146847 restraints weight = 5564.401| |-----------------------------------------------------------------------------| r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.9693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7458 Z= 0.223 Angle : 0.840 13.302 10383 Z= 0.417 Chirality : 0.047 0.207 1238 Planarity : 0.005 0.059 1083 Dihedral : 22.364 168.548 1841 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.20 % Allowed : 26.99 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.57 (0.29), residues: 731 helix: -0.59 (0.25), residues: 348 sheet: -0.96 (0.48), residues: 118 loop : -1.47 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 377 TYR 0.026 0.003 TYR K 190 PHE 0.024 0.003 PHE P 43 TRP 0.027 0.003 TRP K 291 HIS 0.010 0.002 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 7458) covalent geometry : angle 0.84019 (10383) hydrogen bonds : bond 0.06760 ( 357) hydrogen bonds : angle 5.68290 ( 964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.4785 (OUTLIER) cc_final: 0.4514 (ptm) REVERT: B 486 VAL cc_start: 0.8034 (m) cc_final: 0.7593 (t) REVERT: C 115 ASN cc_start: 0.8638 (p0) cc_final: 0.8229 (p0) REVERT: C 138 VAL cc_start: 0.7271 (t) cc_final: 0.7017 (p) REVERT: K 101 ILE cc_start: 0.1692 (OUTLIER) cc_final: 0.1469 (tt) REVERT: K 266 MET cc_start: 0.3108 (tmm) cc_final: 0.2580 (ttt) REVERT: K 281 PHE cc_start: 0.6398 (m-80) cc_final: 0.6102 (m-80) REVERT: K 298 LYS cc_start: 0.7006 (tttt) cc_final: 0.6339 (tptt) outliers start: 32 outliers final: 20 residues processed: 136 average time/residue: 0.0924 time to fit residues: 16.7984 Evaluate side-chains 116 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 303 MET Chi-restraints excluded: chain K residue 311 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.165523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.137942 restraints weight = 20552.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.142244 restraints weight = 11925.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.144959 restraints weight = 8265.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.146764 restraints weight = 6431.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.147990 restraints weight = 5383.011| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 1.0115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7458 Z= 0.157 Angle : 0.762 13.681 10383 Z= 0.377 Chirality : 0.044 0.167 1238 Planarity : 0.004 0.035 1083 Dihedral : 22.131 168.904 1841 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.93 % Allowed : 30.73 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.48 (0.29), residues: 731 helix: -0.48 (0.25), residues: 356 sheet: -1.01 (0.47), residues: 120 loop : -1.46 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 516 TYR 0.015 0.002 TYR P 24 PHE 0.014 0.002 PHE K 274 TRP 0.026 0.003 TRP K 291 HIS 0.006 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7458) covalent geometry : angle 0.76226 (10383) hydrogen bonds : bond 0.05913 ( 357) hydrogen bonds : angle 5.27926 ( 964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 486 VAL cc_start: 0.8032 (m) cc_final: 0.7634 (t) REVERT: C 9 ARG cc_start: 0.7308 (mmp80) cc_final: 0.6826 (mmp80) REVERT: C 115 ASN cc_start: 0.8634 (p0) cc_final: 0.8226 (p0) REVERT: C 138 VAL cc_start: 0.7245 (t) cc_final: 0.6950 (p) REVERT: K 266 MET cc_start: 0.3291 (tmm) cc_final: 0.3010 (ttt) REVERT: K 298 LYS cc_start: 0.7108 (tttt) cc_final: 0.6480 (tptt) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 0.0841 time to fit residues: 14.9916 Evaluate side-chains 123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 0.1980 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 chunk 58 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.169273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.143486 restraints weight = 21596.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.147831 restraints weight = 11676.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.150594 restraints weight = 7875.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.152415 restraints weight = 6040.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.153747 restraints weight = 4973.891| |-----------------------------------------------------------------------------| r_work (final): 0.4811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 1.0448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7458 Z= 0.147 Angle : 0.755 12.783 10383 Z= 0.373 Chirality : 0.045 0.276 1238 Planarity : 0.004 0.033 1083 Dihedral : 21.972 169.335 1841 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.76 % Allowed : 32.52 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.26 (0.29), residues: 731 helix: -0.35 (0.26), residues: 366 sheet: -0.83 (0.47), residues: 117 loop : -1.35 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 516 TYR 0.023 0.002 TYR B 352 PHE 0.015 0.002 PHE C 27 TRP 0.038 0.003 TRP K 291 HIS 0.006 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7458) covalent geometry : angle 0.75504 (10383) hydrogen bonds : bond 0.05847 ( 357) hydrogen bonds : angle 5.11645 ( 964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 ARG cc_start: 0.7315 (mmp80) cc_final: 0.6848 (mmp80) REVERT: C 60 MET cc_start: 0.4860 (tmm) cc_final: 0.4151 (mtt) REVERT: C 115 ASN cc_start: 0.8663 (p0) cc_final: 0.8263 (p0) REVERT: C 138 VAL cc_start: 0.7026 (t) cc_final: 0.6740 (p) REVERT: K 58 GLU cc_start: 0.7752 (pt0) cc_final: 0.7276 (tt0) REVERT: K 164 TYR cc_start: 0.4641 (m-80) cc_final: 0.4114 (m-80) REVERT: P 55 LYS cc_start: 0.7869 (mmpt) cc_final: 0.7427 (mmmt) outliers start: 17 outliers final: 15 residues processed: 125 average time/residue: 0.0855 time to fit residues: 14.5668 Evaluate side-chains 116 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 HIS ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.167409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.141081 restraints weight = 21237.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.145268 restraints weight = 11808.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.147902 restraints weight = 8121.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.149744 restraints weight = 6304.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.151017 restraints weight = 5230.922| |-----------------------------------------------------------------------------| r_work (final): 0.4781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 moved from start: 1.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7458 Z= 0.156 Angle : 0.771 13.724 10383 Z= 0.377 Chirality : 0.044 0.255 1238 Planarity : 0.004 0.031 1083 Dihedral : 21.928 169.459 1841 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.58 % Allowed : 32.36 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.23 (0.29), residues: 731 helix: -0.28 (0.26), residues: 366 sheet: -0.85 (0.47), residues: 117 loop : -1.38 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 516 TYR 0.020 0.002 TYR B 352 PHE 0.016 0.002 PHE B 487 TRP 0.037 0.003 TRP K 291 HIS 0.006 0.002 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7458) covalent geometry : angle 0.77101 (10383) hydrogen bonds : bond 0.05893 ( 357) hydrogen bonds : angle 5.09871 ( 964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 LYS cc_start: 0.8431 (pptt) cc_final: 0.8078 (pptt) REVERT: C 115 ASN cc_start: 0.8586 (p0) cc_final: 0.8206 (p0) REVERT: C 138 VAL cc_start: 0.7121 (t) cc_final: 0.6810 (p) REVERT: K 298 LYS cc_start: 0.7943 (tttt) cc_final: 0.7622 (tptm) REVERT: P 55 LYS cc_start: 0.7891 (mmpt) cc_final: 0.7424 (mmmt) outliers start: 22 outliers final: 16 residues processed: 123 average time/residue: 0.0876 time to fit residues: 14.6043 Evaluate side-chains 112 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 443 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.166895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.140305 restraints weight = 21561.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.144461 restraints weight = 12110.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.147217 restraints weight = 8315.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.149037 restraints weight = 6444.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.150229 restraints weight = 5392.179| |-----------------------------------------------------------------------------| r_work (final): 0.4773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 1.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7458 Z= 0.160 Angle : 0.801 14.603 10383 Z= 0.392 Chirality : 0.044 0.253 1238 Planarity : 0.004 0.033 1083 Dihedral : 21.906 169.571 1841 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.76 % Allowed : 33.66 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.31 (0.29), residues: 731 helix: -0.43 (0.25), residues: 366 sheet: -0.74 (0.47), residues: 117 loop : -1.35 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 9 TYR 0.018 0.002 TYR B 352 PHE 0.016 0.002 PHE C 27 TRP 0.043 0.003 TRP K 291 HIS 0.025 0.003 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7458) covalent geometry : angle 0.80085 (10383) hydrogen bonds : bond 0.05887 ( 357) hydrogen bonds : angle 5.11932 ( 964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 LYS cc_start: 0.8486 (pptt) cc_final: 0.8157 (pptt) REVERT: C 115 ASN cc_start: 0.8659 (p0) cc_final: 0.8354 (p0) REVERT: C 138 VAL cc_start: 0.7082 (t) cc_final: 0.6792 (p) REVERT: K 164 TYR cc_start: 0.4834 (m-80) cc_final: 0.4406 (m-80) REVERT: K 298 LYS cc_start: 0.8054 (tttt) cc_final: 0.7826 (tptm) REVERT: P 55 LYS cc_start: 0.7897 (mmpt) cc_final: 0.7478 (mmmt) outliers start: 17 outliers final: 15 residues processed: 120 average time/residue: 0.0795 time to fit residues: 13.1299 Evaluate side-chains 113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 313 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 HIS ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5023 r_free = 0.5023 target = 0.167107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.140774 restraints weight = 21564.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.144980 restraints weight = 12026.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.147697 restraints weight = 8240.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.149489 restraints weight = 6368.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.150536 restraints weight = 5303.060| |-----------------------------------------------------------------------------| r_work (final): 0.4777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 1.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7458 Z= 0.159 Angle : 0.806 13.769 10383 Z= 0.396 Chirality : 0.045 0.252 1238 Planarity : 0.004 0.052 1083 Dihedral : 21.881 169.535 1841 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.76 % Allowed : 34.47 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.32 (0.29), residues: 731 helix: -0.43 (0.26), residues: 367 sheet: -0.83 (0.46), residues: 117 loop : -1.35 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 377 TYR 0.018 0.002 TYR K 226 PHE 0.016 0.002 PHE C 27 TRP 0.041 0.003 TRP K 291 HIS 0.009 0.002 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7458) covalent geometry : angle 0.80629 (10383) hydrogen bonds : bond 0.05941 ( 357) hydrogen bonds : angle 5.03745 ( 964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.03 seconds wall clock time: 28 minutes 20.73 seconds (1700.73 seconds total)