Starting phenix.real_space_refine on Wed Mar 12 03:52:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d85_46630/03_2025/9d85_46630_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d85_46630/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9d85_46630/03_2025/9d85_46630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d85_46630/03_2025/9d85_46630.map" model { file = "/net/cci-nas-00/data/ceres_data/9d85_46630/03_2025/9d85_46630_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d85_46630/03_2025/9d85_46630_neut.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} 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: 5.18, per 1000 atoms: 0.72 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: 2.08 Conformation dependent library (CDL) restraints added in 915.7 milliseconds 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: 4.63 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: 3.41 Time building geometry restraints manager: 2.44 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: 0.700 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 30.040 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- 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= 0.321 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 : 27.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.002 TRP P 72 HIS 0.002 0.001 HIS K 106 PHE 0.011 0.001 PHE B 506 TYR 0.019 0.002 TYR K 226 ARG 0.007 0.001 ARG K 163 *********************** 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 : 1.090 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: 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: 0.4348 (mtt) REVERT: C 70 ARG cc_start: 0.5801 (mtt-85) cc_final: 0.5425 (tpt170) REVERT: C 115 ASN cc_start: 0.8670 (p0) cc_final: 0.8457 (p0) 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: 0.2506 time to fit residues: 52.5149 Evaluate side-chains 101 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.3980 chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.0722 ------------------------------------------------------------------------------- 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 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS K 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.178070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.153543 restraints weight = 21133.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.157551 restraints weight = 12036.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.160343 restraints weight = 8088.155| |-----------------------------------------------------------------------------| r_work (final): 0.4788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4788 r_free = 0.4788 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4787 r_free = 0.4787 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5073 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7458 Z= 0.268 Angle : 0.807 7.730 10383 Z= 0.420 Chirality : 0.048 0.201 1238 Planarity : 0.006 0.082 1083 Dihedral : 22.986 168.452 1841 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.60 % Allowed : 14.63 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.30), residues: 731 helix: 0.09 (0.26), residues: 352 sheet: -0.87 (0.52), residues: 99 loop : -1.48 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 291 HIS 0.009 0.003 HIS K 106 PHE 0.028 0.003 PHE B 457 TYR 0.022 0.003 TYR B 510 ARG 0.005 0.001 ARG B 368 *********************** 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 141 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.728 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 451 ASP cc_start: 0.6597 (t70) cc_final: 0.6381 (t0) REVERT: B 461 LYS cc_start: 0.4686 (tptp) cc_final: 0.4019 (tptp) REVERT: B 470 LEU cc_start: 0.6437 (mp) cc_final: 0.5996 (tt) REVERT: B 473 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6349 (mm) REVERT: C 115 ASN cc_start: 0.8646 (p0) cc_final: 0.8117 (p0) REVERT: C 124 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7282 (pm20) REVERT: K 1 MET cc_start: 0.0072 (mmm) cc_final: -0.0579 (tpp) outliers start: 16 outliers final: 8 residues processed: 129 average time/residue: 0.2266 time to fit residues: 38.1575 Evaluate side-chains 102 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 20 ILE 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 67 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 52 optimal weight: 0.0070 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 ASN ** K 132 ASN ** 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 = 0.5141 r_free = 0.5141 target = 0.182090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.157644 restraints weight = 21880.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.162053 restraints weight = 11715.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.165014 restraints weight = 7763.386| |-----------------------------------------------------------------------------| r_work (final): 0.4887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5142 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7458 Z= 0.224 Angle : 0.711 11.974 10383 Z= 0.361 Chirality : 0.044 0.187 1238 Planarity : 0.004 0.037 1083 Dihedral : 22.575 166.983 1841 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.55 % Allowed : 18.37 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.30), residues: 731 helix: 0.18 (0.26), residues: 355 sheet: -0.82 (0.54), residues: 94 loop : -1.40 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 291 HIS 0.005 0.001 HIS K 106 PHE 0.019 0.002 PHE C 21 TYR 0.016 0.002 TYR K 127 ARG 0.007 0.001 ARG K 260 *********************** 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 142 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.826 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: B 461 LYS cc_start: 0.4564 (tptp) cc_final: 0.4187 (tptm) REVERT: C 115 ASN cc_start: 0.8449 (p0) cc_final: 0.7989 (p0) REVERT: K -2 MET cc_start: 0.2687 (tpt) cc_final: 0.1886 (tpt) REVERT: K 1 MET cc_start: -0.0154 (mmm) cc_final: -0.0866 (tpp) REVERT: K 97 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7400 (tp) REVERT: K 164 TYR cc_start: 0.4502 (m-10) cc_final: 0.4139 (m-10) REVERT: K 204 THR cc_start: 0.7266 (m) cc_final: 0.6907 (p) REVERT: K 289 ILE cc_start: 0.3446 (mt) cc_final: 0.2504 (mt) REVERT: K 298 LYS cc_start: 0.5142 (tttt) cc_final: 0.4680 (tttt) outliers start: 28 outliers final: 13 residues processed: 132 average time/residue: 0.2017 time to fit residues: 35.6103 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 : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 ASP 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 85 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 107 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.180869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.156273 restraints weight = 21702.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.160930 restraints weight = 11551.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.163802 restraints weight = 7571.446| |-----------------------------------------------------------------------------| r_work (final): 0.4877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5260 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7458 Z= 0.215 Angle : 0.696 12.086 10383 Z= 0.352 Chirality : 0.043 0.172 1238 Planarity : 0.004 0.037 1083 Dihedral : 22.246 167.372 1841 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.74 % Allowed : 20.65 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.30), residues: 731 helix: 0.19 (0.27), residues: 353 sheet: -0.95 (0.53), residues: 97 loop : -1.35 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP K 291 HIS 0.008 0.002 HIS K 106 PHE 0.021 0.002 PHE P 14 TYR 0.015 0.002 TYR K 190 ARG 0.015 0.001 ARG K 84 *********************** 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 142 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.4890 (tptp) cc_final: 0.4595 (tptm) REVERT: B 470 LEU cc_start: 0.6364 (mp) cc_final: 0.5811 (tt) REVERT: C 115 ASN cc_start: 0.8554 (p0) cc_final: 0.8268 (p0) REVERT: C 119 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7587 (mm-30) REVERT: C 124 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: K -2 MET cc_start: 0.2800 (tpt) cc_final: 0.2192 (tpt) REVERT: K 83 LEU cc_start: 0.7434 (mt) cc_final: 0.7150 (tp) REVERT: K 289 ILE cc_start: 0.2784 (mt) cc_final: 0.2574 (mt) outliers start: 23 outliers final: 14 residues processed: 136 average time/residue: 0.1890 time to fit residues: 34.8406 Evaluate side-chains 114 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.179393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.154552 restraints weight = 21408.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.159052 restraints weight = 11710.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.161858 restraints weight = 7799.817| |-----------------------------------------------------------------------------| r_work (final): 0.4846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 moved from start: 0.6692 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= 0.217 Angle : 0.712 14.001 10383 Z= 0.356 Chirality : 0.043 0.179 1238 Planarity : 0.004 0.049 1083 Dihedral : 22.061 168.715 1841 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.25 % Allowed : 25.69 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.30), residues: 731 helix: 0.24 (0.27), residues: 352 sheet: -0.62 (0.51), residues: 102 loop : -1.32 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 291 HIS 0.004 0.001 HIS K 110 PHE 0.036 0.002 PHE K 228 TYR 0.029 0.002 TYR B 415 ARG 0.004 0.001 ARG B 377 *********************** 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 125 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 470 LEU cc_start: 0.6505 (mp) cc_final: 0.5933 (tt) REVERT: C 115 ASN cc_start: 0.8621 (p0) cc_final: 0.8212 (p0) REVERT: C 119 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 124 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: K 97 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7329 (tp) REVERT: K 296 MET cc_start: 0.1207 (ttm) cc_final: 0.0929 (ttm) outliers start: 20 outliers final: 14 residues processed: 119 average time/residue: 0.1864 time to fit residues: 30.3720 Evaluate side-chains 108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 145 VAL 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 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 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 = 0.5105 r_free = 0.5105 target = 0.178662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.154106 restraints weight = 21391.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.158611 restraints weight = 11893.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.161381 restraints weight = 7941.748| |-----------------------------------------------------------------------------| r_work (final): 0.4858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5419 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7458 Z= 0.195 Angle : 0.703 13.110 10383 Z= 0.350 Chirality : 0.043 0.262 1238 Planarity : 0.004 0.038 1083 Dihedral : 21.888 169.351 1841 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.58 % Allowed : 28.46 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.30), residues: 731 helix: 0.12 (0.27), residues: 353 sheet: -0.72 (0.50), residues: 107 loop : -1.34 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 503 HIS 0.004 0.001 HIS B 495 PHE 0.011 0.002 PHE P 43 TYR 0.028 0.002 TYR K 314 ARG 0.004 0.000 ARG K 237 *********************** 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 124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.4553 (mtm) cc_final: 0.4090 (ptm) REVERT: C 115 ASN cc_start: 0.8633 (p0) cc_final: 0.8235 (p0) REVERT: C 124 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7101 (pm20) REVERT: K 97 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7204 (tp) REVERT: K 266 MET cc_start: 0.1142 (tmm) cc_final: -0.0900 (ttt) outliers start: 22 outliers final: 14 residues processed: 119 average time/residue: 0.1710 time to fit residues: 28.0812 Evaluate side-chains 103 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** 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 = 0.5089 r_free = 0.5089 target = 0.176458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.150927 restraints weight = 21053.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.155311 restraints weight = 11895.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.158170 restraints weight = 8107.421| |-----------------------------------------------------------------------------| r_work (final): 0.4833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5539 moved from start: 0.8047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7458 Z= 0.212 Angle : 0.713 11.858 10383 Z= 0.355 Chirality : 0.043 0.240 1238 Planarity : 0.004 0.030 1083 Dihedral : 21.760 169.581 1841 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.88 % Allowed : 26.18 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.31), residues: 731 helix: 0.22 (0.27), residues: 351 sheet: -0.94 (0.46), residues: 120 loop : -1.18 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 503 HIS 0.007 0.001 HIS B 449 PHE 0.032 0.002 PHE K 228 TYR 0.018 0.002 TYR K 190 ARG 0.003 0.000 ARG K 237 *********************** 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 133 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 ASN cc_start: 0.8714 (p0) cc_final: 0.8286 (p0) REVERT: C 119 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7596 (mm-30) REVERT: C 121 LEU cc_start: 0.7701 (mm) cc_final: 0.7236 (tp) REVERT: C 124 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: K 97 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7160 (tp) REVERT: K 207 MET cc_start: 0.4473 (mmp) cc_final: 0.4197 (mmp) REVERT: K 266 MET cc_start: 0.1192 (tmm) cc_final: -0.0838 (ttt) outliers start: 30 outliers final: 18 residues processed: 129 average time/residue: 0.1818 time to fit residues: 32.5304 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 : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 311 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 19 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 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** K 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.175104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.149142 restraints weight = 21493.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.153582 restraints weight = 12180.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.156399 restraints weight = 8246.720| |-----------------------------------------------------------------------------| r_work (final): 0.4783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 moved from start: 0.8600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7458 Z= 0.214 Angle : 0.727 13.044 10383 Z= 0.362 Chirality : 0.043 0.260 1238 Planarity : 0.004 0.031 1083 Dihedral : 21.706 169.890 1841 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.58 % Allowed : 28.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.30), residues: 731 helix: 0.08 (0.27), residues: 350 sheet: -0.94 (0.46), residues: 120 loop : -1.19 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 291 HIS 0.008 0.002 HIS B 495 PHE 0.029 0.002 PHE K 228 TYR 0.019 0.002 TYR K 190 ARG 0.005 0.001 ARG B 516 *********************** 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 133 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 374 GLU cc_start: 0.6491 (mm-30) cc_final: 0.6281 (mm-30) REVERT: C 115 ASN cc_start: 0.8708 (p0) cc_final: 0.8285 (p0) REVERT: C 119 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7460 (mm-30) REVERT: C 123 ARG cc_start: 0.6980 (mtp85) cc_final: 0.5041 (mmp-170) REVERT: C 124 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6989 (pm20) REVERT: K 1 MET cc_start: 0.0561 (tpp) cc_final: -0.0367 (tpt) REVERT: K 207 MET cc_start: 0.4407 (mmp) cc_final: 0.4153 (mmp) REVERT: K 266 MET cc_start: 0.1117 (tmm) cc_final: -0.0665 (ttt) outliers start: 22 outliers final: 16 residues processed: 126 average time/residue: 0.1765 time to fit residues: 30.7198 Evaluate side-chains 113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 311 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4968 r_free = 0.4968 target = 0.164166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.135036 restraints weight = 20637.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.139136 restraints weight = 11924.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.141809 restraints weight = 8301.167| |-----------------------------------------------------------------------------| r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 1.0012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 7458 Z= 0.338 Angle : 0.853 13.081 10383 Z= 0.429 Chirality : 0.049 0.328 1238 Planarity : 0.005 0.035 1083 Dihedral : 21.959 168.964 1841 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.58 % Allowed : 28.94 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.30), residues: 731 helix: -0.44 (0.27), residues: 348 sheet: -0.43 (0.54), residues: 91 loop : -1.53 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP K 291 HIS 0.008 0.002 HIS C 43 PHE 0.033 0.003 PHE K 281 TYR 0.031 0.003 TYR K 190 ARG 0.005 0.001 ARG K 260 *********************** 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 130 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.716 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 413 MET cc_start: 0.4981 (mtm) cc_final: 0.4216 (ptp) REVERT: C 115 ASN cc_start: 0.8738 (p0) cc_final: 0.8292 (p0) REVERT: C 117 ASP cc_start: 0.8084 (m-30) cc_final: 0.7686 (m-30) REVERT: C 119 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7569 (mm-30) REVERT: C 124 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: C 138 VAL cc_start: 0.7279 (t) cc_final: 0.6999 (p) REVERT: K 1 MET cc_start: 0.2349 (tpp) cc_final: 0.1406 (tpp) REVERT: K 101 ILE cc_start: 0.2693 (tt) cc_final: 0.2204 (tt) REVERT: K 207 MET cc_start: 0.4783 (mmp) cc_final: 0.4582 (mmp) REVERT: K 266 MET cc_start: 0.2598 (tmm) cc_final: 0.1414 (ttt) REVERT: K 298 LYS cc_start: 0.6660 (tttt) cc_final: 0.6087 (tptt) outliers start: 22 outliers final: 19 residues processed: 125 average time/residue: 0.1986 time to fit residues: 33.5397 Evaluate side-chains 116 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 C residue 17 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** K 224 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 = 0.5016 r_free = 0.5016 target = 0.167589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.139440 restraints weight = 20880.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.143690 restraints weight = 11744.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.146542 restraints weight = 8020.968| |-----------------------------------------------------------------------------| r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 1.0361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7458 Z= 0.215 Angle : 0.774 13.217 10383 Z= 0.387 Chirality : 0.045 0.252 1238 Planarity : 0.004 0.032 1083 Dihedral : 21.798 169.832 1841 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.44 % Allowed : 31.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.30), residues: 731 helix: -0.34 (0.26), residues: 355 sheet: -0.83 (0.47), residues: 120 loop : -1.43 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP K 291 HIS 0.005 0.002 HIS C 40 PHE 0.019 0.002 PHE K 281 TYR 0.017 0.002 TYR B 387 ARG 0.005 0.001 ARG B 516 ********************** 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 123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.5342 (mtm) cc_final: 0.4762 (ptm) REVERT: C 115 ASN cc_start: 0.8657 (p0) cc_final: 0.8174 (p0) REVERT: C 117 ASP cc_start: 0.8039 (m-30) cc_final: 0.7675 (m-30) REVERT: C 119 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7442 (mm-30) REVERT: C 123 ARG cc_start: 0.7090 (mtp85) cc_final: 0.5554 (mpt180) REVERT: C 124 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: K 1 MET cc_start: 0.1907 (tpp) cc_final: 0.1571 (tpt) REVERT: K 184 LYS cc_start: 0.4592 (pttp) cc_final: 0.4138 (mmmt) REVERT: K 248 MET cc_start: 0.5422 (mmm) cc_final: 0.5129 (mmm) REVERT: K 266 MET cc_start: 0.2673 (tmm) cc_final: 0.1700 (ttt) REVERT: K 298 LYS cc_start: 0.6782 (tttt) cc_final: 0.6461 (tptt) outliers start: 15 outliers final: 13 residues processed: 119 average time/residue: 0.2102 time to fit residues: 33.3447 Evaluate side-chains 112 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 259 LEU 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 50 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 0.0670 chunk 56 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.169036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.141218 restraints weight = 20890.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.145580 restraints weight = 11589.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.148445 restraints weight = 7915.328| |-----------------------------------------------------------------------------| r_work (final): 0.4772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 1.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7458 Z= 0.206 Angle : 0.758 13.212 10383 Z= 0.380 Chirality : 0.044 0.245 1238 Planarity : 0.005 0.067 1083 Dihedral : 21.653 169.697 1841 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.44 % Allowed : 32.36 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.30), residues: 731 helix: -0.33 (0.27), residues: 362 sheet: -0.67 (0.47), residues: 119 loop : -1.58 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP K 291 HIS 0.008 0.001 HIS B 443 PHE 0.015 0.002 PHE K 228 TYR 0.016 0.002 TYR P 24 ARG 0.009 0.001 ARG K 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2937.33 seconds wall clock time: 51 minutes 39.01 seconds (3099.01 seconds total)