Starting phenix.real_space_refine on Wed Feb 12 09:26:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wuh_21913/02_2025/6wuh_21913.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wuh_21913/02_2025/6wuh_21913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wuh_21913/02_2025/6wuh_21913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wuh_21913/02_2025/6wuh_21913.map" model { file = "/net/cci-nas-00/data/ceres_data/6wuh_21913/02_2025/6wuh_21913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wuh_21913/02_2025/6wuh_21913.cif" } resolution = 3.4 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= 0.011 sd= 0.094 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 4930 2.51 5 N 1400 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7790 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2400 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 24, 'TRANS': 283} Chain breaks: 2 Chain: "B" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3176 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2214 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 20, 'TRANS': 273} Chain breaks: 2 Time building chain proxies: 4.44, per 1000 atoms: 0.57 Number of scatterers: 7790 At special positions: 0 Unit cell: (110.24, 89.04, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 1444 8.00 N 1400 7.00 C 4930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 36.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 59 through 64 removed outlier: 4.118A pdb=" N LEU A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.702A pdb=" N LYS A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 150 through 163 removed outlier: 3.536A pdb=" N GLN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 193 through 213 removed outlier: 4.143A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 269 through 285 removed outlier: 4.122A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.611A pdb=" N HIS A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.886A pdb=" N GLN B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.648A pdb=" N GLY B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.857A pdb=" N ASP B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 374 " --> pdb=" O GLY B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.694A pdb=" N THR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 43 through 47 removed outlier: 3.596A pdb=" N VAL C 47 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 removed outlier: 3.581A pdb=" N ILE C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 120 removed outlier: 3.642A pdb=" N SER C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.519A pdb=" N LEU C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.626A pdb=" N TRP C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 239 through 251 removed outlier: 4.612A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 284 removed outlier: 3.746A pdb=" N LEU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 removed outlier: 4.201A pdb=" N ILE C 295 " --> pdb=" O TRP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.755A pdb=" N CYS C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.923A pdb=" N LYS C 320 " --> pdb=" O GLN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.829A pdb=" N ALA C 333 " --> pdb=" O GLN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 356 through 377 removed outlier: 4.646A pdb=" N TRP C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP C 361 " --> pdb=" O VAL C 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain 'B' and resid 139 through 140 removed outlier: 3.566A pdb=" N VAL B 158 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 179 through 182 removed outlier: 6.000A pdb=" N ALA B 207 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS B 215 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 234 through 235 removed outlier: 3.988A pdb=" N THR B 275 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 291 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 400 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 342 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 396 " --> pdb=" O GLY B 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 416 through 417 Processing sheet with id=AA7, first strand: chain 'B' and resid 420 through 423 Processing sheet with id=AA8, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 54 through 56 removed outlier: 3.705A pdb=" N ILE C 64 " --> pdb=" O LEU C 55 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2604 1.34 - 1.46: 1569 1.46 - 1.58: 3766 1.58 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 7966 Sorted by residual: bond pdb=" C ALA B 254 " pdb=" N SER B 255 " ideal model delta sigma weight residual 1.339 1.281 0.058 5.57e-02 3.22e+02 1.08e+00 bond pdb=" C LEU C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.86e-01 bond pdb=" C PHE A 27 " pdb=" N PRO A 28 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.41e-01 bond pdb=" C LYS B 67 " pdb=" N PRO B 68 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.09e-01 bond pdb=" CG LEU B 169 " pdb=" CD2 LEU B 169 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.87e-01 ... (remaining 7961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10532 1.68 - 3.37: 260 3.37 - 5.05: 41 5.05 - 6.74: 7 6.74 - 8.42: 3 Bond angle restraints: 10843 Sorted by residual: angle pdb=" N LEU C 284 " pdb=" CA LEU C 284 " pdb=" C LEU C 284 " ideal model delta sigma weight residual 109.81 117.74 -7.93 2.21e+00 2.05e-01 1.29e+01 angle pdb=" N ILE C 17 " pdb=" CA ILE C 17 " pdb=" C ILE C 17 " ideal model delta sigma weight residual 111.88 108.76 3.12 1.06e+00 8.90e-01 8.67e+00 angle pdb=" N LEU A 101 " pdb=" CA LEU A 101 " pdb=" C LEU A 101 " ideal model delta sigma weight residual 109.81 116.06 -6.25 2.21e+00 2.05e-01 8.00e+00 angle pdb=" C SER A 257 " pdb=" N GLU A 258 " pdb=" CA GLU A 258 " ideal model delta sigma weight residual 125.66 130.44 -4.78 1.85e+00 2.92e-01 6.68e+00 angle pdb=" CA LEU C 52 " pdb=" CB LEU C 52 " pdb=" CG LEU C 52 " ideal model delta sigma weight residual 116.30 107.88 8.42 3.50e+00 8.16e-02 5.79e+00 ... (remaining 10838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4267 17.90 - 35.80: 376 35.80 - 53.70: 77 53.70 - 71.60: 15 71.60 - 89.50: 7 Dihedral angle restraints: 4742 sinusoidal: 1798 harmonic: 2944 Sorted by residual: dihedral pdb=" CA TRP A 261 " pdb=" C TRP A 261 " pdb=" N PHE A 262 " pdb=" CA PHE A 262 " ideal model delta harmonic sigma weight residual 180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ALA B 213 " pdb=" C ALA B 213 " pdb=" N SER B 214 " pdb=" CA SER B 214 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA HIS C 51 " pdb=" C HIS C 51 " pdb=" N LEU C 52 " pdb=" CA LEU C 52 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 4739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 732 0.032 - 0.063: 320 0.063 - 0.095: 106 0.095 - 0.126: 57 0.126 - 0.158: 9 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CB VAL C 287 " pdb=" CA VAL C 287 " pdb=" CG1 VAL C 287 " pdb=" CG2 VAL C 287 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA LEU C 284 " pdb=" N LEU C 284 " pdb=" C LEU C 284 " pdb=" CB LEU C 284 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 1221 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 478 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO B 479 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 159 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO C 160 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 18 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 19 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " 0.025 5.00e-02 4.00e+02 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 256 2.68 - 3.24: 7543 3.24 - 3.79: 11225 3.79 - 4.35: 14611 4.35 - 4.90: 24770 Nonbonded interactions: 58405 Sorted by model distance: nonbonded pdb=" O LEU A 159 " pdb=" OG SER A 163 " model vdw 2.129 3.040 nonbonded pdb=" OG SER B 268 " pdb=" O ASN B 304 " model vdw 2.137 3.040 nonbonded pdb=" O GLY C 328 " pdb=" OG SER C 332 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR C 132 " pdb=" OH TYR C 146 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN B 148 " pdb=" ND2 ASN B 372 " model vdw 2.226 3.120 ... (remaining 58400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.920 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.003 0.058 7966 Z= 0.227 Angle : 0.668 8.419 10843 Z= 0.364 Chirality : 0.043 0.158 1224 Planarity : 0.005 0.055 1412 Dihedral : 14.686 89.502 2852 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.49 % Favored : 87.51 % Rotamer: Outliers : 5.42 % Allowed : 14.38 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.22), residues: 1017 helix: -1.63 (0.25), residues: 340 sheet: -4.48 (0.27), residues: 193 loop : -4.23 (0.22), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 258 HIS 0.005 0.001 HIS C 6 PHE 0.015 0.001 PHE A 68 TYR 0.010 0.001 TYR B 240 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.893 Fit side-chains REVERT: A 206 ARG cc_start: 0.7331 (ttp-170) cc_final: 0.6917 (mmt-90) REVERT: A 258 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: C 115 TYR cc_start: 0.8909 (m-80) cc_final: 0.8700 (m-80) REVERT: C 257 ASP cc_start: 0.8541 (t0) cc_final: 0.8323 (t0) outliers start: 43 outliers final: 27 residues processed: 161 average time/residue: 0.2233 time to fit residues: 47.2103 Evaluate side-chains 118 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 353 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.0030 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 0.0770 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 166 ASN A 178 HIS B 64 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 286 GLN B 367 GLN B 419 GLN B 463 ASN C 4 GLN C 6 HIS C 137 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132423 restraints weight = 9825.946| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.55 r_work: 0.3346 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7966 Z= 0.192 Angle : 0.654 9.637 10843 Z= 0.326 Chirality : 0.043 0.160 1224 Planarity : 0.006 0.055 1412 Dihedral : 8.565 77.145 1174 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % Rotamer: Outliers : 5.17 % Allowed : 17.28 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.25), residues: 1017 helix: -0.39 (0.29), residues: 340 sheet: -3.95 (0.31), residues: 183 loop : -3.77 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 8 HIS 0.005 0.001 HIS C 172 PHE 0.011 0.001 PHE A 68 TYR 0.011 0.001 TYR A 240 ARG 0.005 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.899 Fit side-chains REVERT: A 26 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8186 (t80) REVERT: A 206 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.6837 (mmt-90) REVERT: B 275 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8720 (p) REVERT: B 419 GLN cc_start: 0.6926 (tt0) cc_final: 0.6664 (tt0) REVERT: C 27 TYR cc_start: 0.8440 (t80) cc_final: 0.8203 (t80) REVERT: C 51 HIS cc_start: 0.7399 (t-170) cc_final: 0.7181 (t-90) outliers start: 41 outliers final: 27 residues processed: 139 average time/residue: 0.1673 time to fit residues: 33.5736 Evaluate side-chains 120 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN C 50 GLN C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131498 restraints weight = 9888.496| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.64 r_work: 0.3342 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7966 Z= 0.271 Angle : 0.675 11.088 10843 Z= 0.333 Chirality : 0.044 0.165 1224 Planarity : 0.006 0.058 1412 Dihedral : 7.732 77.534 1155 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 7.06 % Allowed : 18.28 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.26), residues: 1017 helix: 0.02 (0.30), residues: 342 sheet: -3.80 (0.32), residues: 185 loop : -3.60 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 258 HIS 0.006 0.001 HIS C 172 PHE 0.019 0.001 PHE A 68 TYR 0.011 0.001 TYR A 240 ARG 0.006 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 97 time to evaluate : 0.831 Fit side-chains REVERT: A 26 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8314 (t80) REVERT: A 27 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.7041 (t80) REVERT: A 206 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.6884 (mmt-90) REVERT: B 275 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8810 (p) REVERT: C 51 HIS cc_start: 0.7537 (t-170) cc_final: 0.7294 (t-90) REVERT: C 353 GLU cc_start: 0.7310 (tp30) cc_final: 0.7034 (tp30) outliers start: 56 outliers final: 36 residues processed: 142 average time/residue: 0.1637 time to fit residues: 33.0619 Evaluate side-chains 133 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 8 optimal weight: 0.0570 chunk 98 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 96 optimal weight: 3.9990 overall best weight: 0.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 82 GLN C 50 GLN C 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.172864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136558 restraints weight = 9756.727| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.67 r_work: 0.3380 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7966 Z= 0.168 Angle : 0.622 11.217 10843 Z= 0.306 Chirality : 0.042 0.157 1224 Planarity : 0.005 0.060 1412 Dihedral : 7.201 77.678 1153 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 5.30 % Allowed : 19.29 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.26), residues: 1017 helix: 0.41 (0.30), residues: 336 sheet: -3.61 (0.33), residues: 179 loop : -3.41 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 258 HIS 0.005 0.001 HIS C 172 PHE 0.013 0.001 PHE A 24 TYR 0.013 0.001 TYR A 240 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.793 Fit side-chains REVERT: A 26 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8180 (t80) REVERT: A 27 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6821 (t80) REVERT: A 206 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.6747 (mmt-90) REVERT: B 155 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8641 (p) REVERT: B 160 ARG cc_start: 0.7869 (mmt-90) cc_final: 0.7629 (mmm160) REVERT: B 275 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8707 (p) REVERT: C 36 ASP cc_start: 0.7575 (m-30) cc_final: 0.7365 (m-30) REVERT: C 257 ASP cc_start: 0.8603 (t0) cc_final: 0.8394 (t0) outliers start: 42 outliers final: 26 residues processed: 138 average time/residue: 0.1737 time to fit residues: 34.4630 Evaluate side-chains 125 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 77 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 HIS C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.171665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135306 restraints weight = 9717.745| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.56 r_work: 0.3411 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7966 Z= 0.188 Angle : 0.633 12.793 10843 Z= 0.304 Chirality : 0.042 0.152 1224 Planarity : 0.005 0.060 1412 Dihedral : 6.780 77.313 1149 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 5.30 % Allowed : 20.43 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.27), residues: 1017 helix: 0.60 (0.31), residues: 336 sheet: -3.50 (0.34), residues: 181 loop : -3.32 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 8 HIS 0.006 0.001 HIS C 75 PHE 0.013 0.001 PHE A 68 TYR 0.013 0.001 TYR A 240 ARG 0.006 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8334 (t80) REVERT: A 27 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6939 (t80) REVERT: A 206 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.6890 (mmt-90) REVERT: B 155 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8705 (p) REVERT: B 160 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.7741 (mmm160) REVERT: B 275 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8777 (p) REVERT: C 36 ASP cc_start: 0.7629 (m-30) cc_final: 0.7415 (m-30) REVERT: C 257 ASP cc_start: 0.8703 (t0) cc_final: 0.8448 (t0) outliers start: 42 outliers final: 32 residues processed: 132 average time/residue: 0.1737 time to fit residues: 32.5118 Evaluate side-chains 128 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 55 optimal weight: 0.0470 chunk 39 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN C 75 HIS C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.170715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134211 restraints weight = 9838.196| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.68 r_work: 0.3388 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7966 Z= 0.222 Angle : 0.648 11.459 10843 Z= 0.310 Chirality : 0.042 0.153 1224 Planarity : 0.005 0.062 1412 Dihedral : 6.794 77.207 1148 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 6.31 % Allowed : 19.04 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.27), residues: 1017 helix: 0.60 (0.30), residues: 346 sheet: -3.53 (0.33), residues: 186 loop : -3.27 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 8 HIS 0.006 0.001 HIS C 75 PHE 0.015 0.001 PHE A 68 TYR 0.014 0.001 TYR A 240 ARG 0.006 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.8271 (t80) REVERT: A 27 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6959 (t80) REVERT: A 206 ARG cc_start: 0.7918 (ttp-170) cc_final: 0.6915 (mmt180) REVERT: B 155 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8751 (p) REVERT: B 275 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8770 (p) REVERT: C 166 MET cc_start: 0.8449 (tpp) cc_final: 0.8140 (tpt) REVERT: C 257 ASP cc_start: 0.8763 (t0) cc_final: 0.8491 (t0) outliers start: 50 outliers final: 35 residues processed: 139 average time/residue: 0.1794 time to fit residues: 35.0360 Evaluate side-chains 135 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 HIS C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134432 restraints weight = 9796.131| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.70 r_work: 0.3384 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7966 Z= 0.204 Angle : 0.643 11.784 10843 Z= 0.308 Chirality : 0.042 0.148 1224 Planarity : 0.006 0.063 1412 Dihedral : 6.644 77.074 1148 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 5.80 % Allowed : 20.30 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.27), residues: 1017 helix: 0.62 (0.30), residues: 346 sheet: -3.45 (0.33), residues: 191 loop : -3.20 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 8 HIS 0.006 0.001 HIS C 75 PHE 0.014 0.001 PHE A 68 TYR 0.010 0.001 TYR A 240 ARG 0.008 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8239 (t80) REVERT: A 27 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6980 (t80) REVERT: A 206 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.6828 (mmt-90) REVERT: B 155 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8713 (p) REVERT: B 160 ARG cc_start: 0.8015 (mmt-90) cc_final: 0.7693 (mmm160) REVERT: B 275 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8753 (p) REVERT: C 37 TYR cc_start: 0.8701 (p90) cc_final: 0.8242 (p90) REVERT: C 166 MET cc_start: 0.8425 (tpp) cc_final: 0.8146 (tpt) REVERT: C 257 ASP cc_start: 0.8778 (t0) cc_final: 0.8448 (t0) outliers start: 46 outliers final: 39 residues processed: 136 average time/residue: 0.1790 time to fit residues: 34.5168 Evaluate side-chains 136 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 93 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 356 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.3980 chunk 96 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 85 optimal weight: 0.0270 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN C 75 HIS C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.173583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137952 restraints weight = 9626.158| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.56 r_work: 0.3416 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7966 Z= 0.168 Angle : 0.652 11.735 10843 Z= 0.307 Chirality : 0.042 0.155 1224 Planarity : 0.005 0.062 1412 Dihedral : 6.428 76.921 1148 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 5.30 % Allowed : 21.19 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.27), residues: 1017 helix: 0.68 (0.30), residues: 348 sheet: -3.36 (0.33), residues: 191 loop : -3.15 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 8 HIS 0.006 0.001 HIS C 75 PHE 0.009 0.001 PHE A 68 TYR 0.009 0.001 TYR C 37 ARG 0.007 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8239 (t80) REVERT: A 27 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6963 (t80) REVERT: A 185 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 206 ARG cc_start: 0.7891 (ttp-170) cc_final: 0.6851 (mmt-90) REVERT: B 155 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8690 (p) REVERT: B 160 ARG cc_start: 0.7987 (mmt-90) cc_final: 0.7661 (mmm160) REVERT: B 275 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8700 (p) REVERT: C 37 TYR cc_start: 0.8590 (p90) cc_final: 0.8211 (p90) REVERT: C 166 MET cc_start: 0.8377 (tpp) cc_final: 0.8109 (tpt) REVERT: C 257 ASP cc_start: 0.8764 (t0) cc_final: 0.8464 (t0) outliers start: 42 outliers final: 34 residues processed: 132 average time/residue: 0.1737 time to fit residues: 32.3355 Evaluate side-chains 130 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 30 optimal weight: 0.0040 chunk 66 optimal weight: 9.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 HIS C 75 HIS C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.174344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138487 restraints weight = 9819.744| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.59 r_work: 0.3422 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7966 Z= 0.178 Angle : 0.652 11.050 10843 Z= 0.307 Chirality : 0.042 0.155 1224 Planarity : 0.006 0.063 1412 Dihedral : 6.203 76.731 1147 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 5.17 % Allowed : 21.31 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.27), residues: 1017 helix: 0.66 (0.29), residues: 354 sheet: -3.27 (0.32), residues: 202 loop : -3.11 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 8 HIS 0.006 0.001 HIS C 75 PHE 0.010 0.001 PHE A 68 TYR 0.016 0.001 TYR B 240 ARG 0.007 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8240 (t80) REVERT: A 27 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6988 (t80) REVERT: A 185 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8653 (mp) REVERT: A 206 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.6831 (mmt-90) REVERT: B 155 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8708 (p) REVERT: B 160 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.7660 (mmm160) REVERT: B 275 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8695 (p) REVERT: B 406 PRO cc_start: 0.8108 (Cg_exo) cc_final: 0.7902 (Cg_endo) REVERT: C 37 TYR cc_start: 0.8534 (p90) cc_final: 0.8195 (p90) REVERT: C 166 MET cc_start: 0.8402 (tpp) cc_final: 0.8149 (tpt) REVERT: C 257 ASP cc_start: 0.8764 (t0) cc_final: 0.8481 (t0) outliers start: 41 outliers final: 33 residues processed: 132 average time/residue: 0.1699 time to fit residues: 31.8197 Evaluate side-chains 132 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 353 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 HIS C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.173124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.137412 restraints weight = 9720.591| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.56 r_work: 0.3395 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7966 Z= 0.215 Angle : 0.678 12.289 10843 Z= 0.319 Chirality : 0.042 0.146 1224 Planarity : 0.006 0.063 1412 Dihedral : 6.297 76.634 1147 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 4.92 % Allowed : 21.69 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.27), residues: 1017 helix: 0.77 (0.30), residues: 348 sheet: -3.30 (0.33), residues: 191 loop : -3.06 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 8 HIS 0.006 0.001 HIS C 75 PHE 0.012 0.001 PHE A 68 TYR 0.015 0.001 TYR B 240 ARG 0.006 0.000 ARG A 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8224 (t80) REVERT: A 27 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6846 (t80) REVERT: A 185 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8671 (mp) REVERT: A 206 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.6779 (mmt-90) REVERT: B 155 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 275 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8631 (p) REVERT: B 375 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7625 (mpp80) REVERT: B 406 PRO cc_start: 0.7991 (Cg_exo) cc_final: 0.7765 (Cg_endo) REVERT: C 37 TYR cc_start: 0.8493 (p90) cc_final: 0.8202 (p90) REVERT: C 166 MET cc_start: 0.8357 (tpp) cc_final: 0.8113 (tpt) REVERT: C 257 ASP cc_start: 0.8746 (t0) cc_final: 0.8511 (t0) outliers start: 39 outliers final: 34 residues processed: 126 average time/residue: 0.1696 time to fit residues: 30.4778 Evaluate side-chains 135 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 353 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 chunk 45 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN C 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136526 restraints weight = 9725.801| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.59 r_work: 0.3390 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 7966 Z= 0.267 Angle : 1.021 59.178 10843 Z= 0.588 Chirality : 0.043 0.331 1224 Planarity : 0.006 0.063 1412 Dihedral : 6.301 76.644 1147 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 5.30 % Allowed : 21.82 % Favored : 72.89 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.27), residues: 1017 helix: 0.80 (0.30), residues: 348 sheet: -3.30 (0.33), residues: 191 loop : -3.06 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 8 HIS 0.006 0.001 HIS C 75 PHE 0.012 0.001 PHE A 68 TYR 0.014 0.001 TYR B 240 ARG 0.005 0.000 ARG C 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3987.46 seconds wall clock time: 71 minutes 19.33 seconds (4279.33 seconds total)