Starting phenix.real_space_refine on Tue Feb 11 22:06:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f46_31444/02_2025/7f46_31444.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f46_31444/02_2025/7f46_31444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f46_31444/02_2025/7f46_31444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f46_31444/02_2025/7f46_31444.map" model { file = "/net/cci-nas-00/data/ceres_data/7f46_31444/02_2025/7f46_31444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f46_31444/02_2025/7f46_31444.cif" } resolution = 4.79 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= 0.001 sd= 0.015 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 25 5.16 5 C 4187 2.51 5 N 1091 2.21 5 O 1261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 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: 6564 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1652 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 10, 'TRANS': 192} Chain breaks: 4 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.74, per 1000 atoms: 0.72 Number of scatterers: 6564 At special positions: 0 Unit cell: (91.98, 82.125, 129.21, 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 25 16.00 O 1261 8.00 N 1091 7.00 C 4187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG C1301 " - " ASN C 165 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 991.7 milliseconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 6.3% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.520A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.520A pdb=" N ALA B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.529A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 5.674A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.761A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.905A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'L' and resid 126 through 130 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.726A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.174A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.723A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.603A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.668A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.009A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 167 through 171 Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.563A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.918A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.771A pdb=" N VAL L 155 " --> pdb=" O ALA L 158 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 546 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: 2.04 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2075 1.34 - 1.46: 1637 1.46 - 1.58: 2986 1.58 - 1.71: 0 1.71 - 1.83: 31 Bond restraints: 6729 Sorted by residual: bond pdb=" N LEU H 206 " pdb=" CA LEU H 206 " ideal model delta sigma weight residual 1.458 1.503 -0.046 1.27e-02 6.20e+03 1.29e+01 bond pdb=" N VAL B 524 " pdb=" CA VAL B 524 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.96e+00 bond pdb=" N LYS H 76 " pdb=" CA LYS H 76 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.16e-02 7.43e+03 9.70e+00 bond pdb=" N VAL H 103 " pdb=" CA VAL H 103 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 8.96e+00 bond pdb=" N VAL B 483 " pdb=" CA VAL B 483 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.21e-02 6.83e+03 8.86e+00 ... (remaining 6724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 8293 1.33 - 2.66: 678 2.66 - 3.99: 146 3.99 - 5.31: 30 5.31 - 6.64: 9 Bond angle restraints: 9156 Sorted by residual: angle pdb=" N SER H 204 " pdb=" CA SER H 204 " pdb=" C SER H 204 " ideal model delta sigma weight residual 112.38 107.89 4.49 1.22e+00 6.72e-01 1.35e+01 angle pdb=" CA CYS C 166 " pdb=" C CYS C 166 " pdb=" O CYS C 166 " ideal model delta sigma weight residual 121.40 117.34 4.06 1.13e+00 7.83e-01 1.29e+01 angle pdb=" CA SER B 477 " pdb=" C SER B 477 " pdb=" O SER B 477 " ideal model delta sigma weight residual 122.13 118.24 3.89 1.13e+00 7.83e-01 1.18e+01 angle pdb=" N LYS C 187 " pdb=" CA LYS C 187 " pdb=" C LYS C 187 " ideal model delta sigma weight residual 113.89 108.54 5.35 1.58e+00 4.01e-01 1.14e+01 angle pdb=" N SER L 57 " pdb=" CA SER L 57 " pdb=" C SER L 57 " ideal model delta sigma weight residual 114.56 110.32 4.24 1.27e+00 6.20e-01 1.12e+01 ... (remaining 9151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 3578 17.08 - 34.15: 347 34.15 - 51.23: 54 51.23 - 68.31: 10 68.31 - 85.38: 3 Dihedral angle restraints: 3992 sinusoidal: 1559 harmonic: 2433 Sorted by residual: dihedral pdb=" CB CYS H 157 " pdb=" SG CYS H 157 " pdb=" SG CYS H 213 " pdb=" CB CYS H 213 " ideal model delta sinusoidal sigma weight residual 93.00 141.24 -48.24 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 48.52 44.48 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 677 0.045 - 0.089: 243 0.089 - 0.134: 77 0.134 - 0.178: 18 0.178 - 0.222: 4 Chirality restraints: 1019 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ALA C 222 " pdb=" N ALA C 222 " pdb=" C ALA C 222 " pdb=" CB ALA C 222 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA LEU H 206 " pdb=" N LEU H 206 " pdb=" C LEU H 206 " pdb=" CB LEU H 206 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 1016 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.287 2.00e-02 2.50e+03 2.46e-01 7.56e+02 pdb=" C7 NAG B1301 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " 0.017 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.414 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " 0.257 2.00e-02 2.50e+03 2.14e-01 5.71e+02 pdb=" C7 NAG C1301 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " -0.355 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 224 " -0.065 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO C 225 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " -0.054 5.00e-02 4.00e+02 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 908 2.75 - 3.29: 6132 3.29 - 3.83: 9898 3.83 - 4.36: 11286 4.36 - 4.90: 20294 Nonbonded interactions: 48518 Sorted by model distance: nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.218 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.220 3.040 nonbonded pdb=" O PHE C 106 " pdb=" OG SER C 116 " model vdw 2.223 3.040 nonbonded pdb=" OG SER B 443 " pdb=" O PHE B 497 " model vdw 2.277 3.040 nonbonded pdb=" O ARG L 147 " pdb=" NH1 ARG L 147 " model vdw 2.304 3.120 ... (remaining 48513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.590 Find NCS groups from input model: 0.130 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 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 : 0.006 0.054 6729 Z= 0.377 Angle : 0.840 6.643 9156 Z= 0.507 Chirality : 0.053 0.222 1019 Planarity : 0.011 0.246 1178 Dihedral : 13.319 85.382 2412 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -2.90 (0.27), residues: 822 helix: -3.98 (0.66), residues: 25 sheet: -0.97 (0.27), residues: 327 loop : -2.62 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.020 0.002 PHE H 139 TYR 0.034 0.002 TYR B 473 ARG 0.005 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.713 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: C 53 ASP cc_start: 0.8147 (m-30) cc_final: 0.7851 (m-30) REVERT: H 83 MET cc_start: 0.5586 (mtm) cc_final: 0.4143 (mtm) REVERT: H 102 MET cc_start: 0.0415 (ppp) cc_final: -0.0067 (mpp) REVERT: H 117 MET cc_start: 0.6580 (mtt) cc_final: 0.5373 (mmp) REVERT: H 198 VAL cc_start: 0.1912 (p) cc_final: 0.1363 (t) REVERT: L 41 TYR cc_start: 0.6811 (m-80) cc_final: 0.6403 (m-80) REVERT: L 91 TYR cc_start: 0.6202 (m-10) cc_final: 0.5704 (m-10) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1672 time to fit residues: 17.5077 Evaluate side-chains 40 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS C 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 203 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.142913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.091909 restraints weight = 40581.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.084515 restraints weight = 42011.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.083570 restraints weight = 33124.214| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6729 Z= 0.255 Angle : 0.687 6.724 9156 Z= 0.364 Chirality : 0.046 0.217 1019 Planarity : 0.006 0.071 1178 Dihedral : 5.576 31.269 950 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.28 % Allowed : 7.03 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -2.45 (0.28), residues: 822 helix: -3.67 (0.90), residues: 19 sheet: -0.66 (0.28), residues: 331 loop : -2.35 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 53 HIS 0.007 0.002 HIS H 82 PHE 0.015 0.002 PHE L 121 TYR 0.019 0.002 TYR L 145 ARG 0.005 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.0319 (ppp) cc_final: 0.0023 (mpp) REVERT: L 53 ILE cc_start: 0.2667 (mt) cc_final: 0.1543 (mt) REVERT: L 77 THR cc_start: 0.4364 (p) cc_final: 0.4139 (p) REVERT: L 94 MET cc_start: 0.7811 (ttt) cc_final: 0.7291 (tmm) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.1564 time to fit residues: 13.8448 Evaluate side-chains 34 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 0.0020 chunk 51 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 50 GLN L 165 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.137937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.081626 restraints weight = 39512.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.080945 restraints weight = 31228.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.080090 restraints weight = 29594.723| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 6729 Z= 0.331 Angle : 0.816 10.925 9156 Z= 0.426 Chirality : 0.049 0.292 1019 Planarity : 0.007 0.087 1178 Dihedral : 6.481 39.280 950 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -2.38 (0.28), residues: 822 helix: -3.85 (0.67), residues: 25 sheet: -0.72 (0.28), residues: 324 loop : -2.15 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 353 HIS 0.011 0.002 HIS B 519 PHE 0.021 0.003 PHE L 103 TYR 0.051 0.003 TYR L 145 ARG 0.007 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.1695 (ppp) cc_final: 0.1212 (mpp) REVERT: H 198 VAL cc_start: 0.3420 (p) cc_final: 0.3175 (t) REVERT: L 178 TYR cc_start: -0.0018 (m-80) cc_final: -0.0278 (m-80) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1397 time to fit residues: 9.9149 Evaluate side-chains 37 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.0010 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN L 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.141333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.086035 restraints weight = 62998.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.085141 restraints weight = 53786.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.086741 restraints weight = 43070.881| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6729 Z= 0.245 Angle : 0.686 7.702 9156 Z= 0.359 Chirality : 0.046 0.252 1019 Planarity : 0.006 0.093 1178 Dihedral : 5.769 28.282 950 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -2.23 (0.28), residues: 822 helix: -3.98 (0.77), residues: 19 sheet: -0.62 (0.28), residues: 329 loop : -2.08 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 64 HIS 0.016 0.002 HIS C 66 PHE 0.014 0.002 PHE L 144 TYR 0.035 0.002 TYR C 266 ARG 0.008 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.8277 (t0) cc_final: 0.8024 (t70) REVERT: B 456 PHE cc_start: 0.9304 (m-80) cc_final: 0.8987 (m-80) REVERT: B 505 TYR cc_start: 0.9028 (m-80) cc_final: 0.8687 (t80) REVERT: H 102 MET cc_start: 0.1255 (ppp) cc_final: 0.0999 (mpp) REVERT: L 91 TYR cc_start: 0.5427 (m-10) cc_final: 0.5056 (m-10) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1585 time to fit residues: 12.3326 Evaluate side-chains 39 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 4 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 43 optimal weight: 0.0040 chunk 75 optimal weight: 0.0870 chunk 49 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** 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 = 0.4355 r_free = 0.4355 target = 0.143121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.098202 restraints weight = 62399.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.095943 restraints weight = 61540.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.094689 restraints weight = 47180.786| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 6729 Z= 0.156 Angle : 0.595 9.974 9156 Z= 0.306 Chirality : 0.044 0.174 1019 Planarity : 0.005 0.089 1178 Dihedral : 4.997 24.839 950 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.97 (0.28), residues: 822 helix: -3.63 (0.75), residues: 25 sheet: -0.34 (0.28), residues: 326 loop : -1.95 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 64 HIS 0.013 0.001 HIS C 66 PHE 0.014 0.001 PHE L 144 TYR 0.019 0.001 TYR C 266 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.7974 (t0) cc_final: 0.7716 (t70) REVERT: B 456 PHE cc_start: 0.9390 (m-80) cc_final: 0.9027 (m-80) REVERT: B 505 TYR cc_start: 0.8930 (m-80) cc_final: 0.8649 (t80) REVERT: H 102 MET cc_start: 0.1652 (ppp) cc_final: 0.1103 (mpp) REVERT: L 91 TYR cc_start: 0.5901 (m-10) cc_final: 0.5520 (m-10) REVERT: L 94 MET cc_start: 0.3322 (mmp) cc_final: 0.2841 (mmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1648 time to fit residues: 9.8868 Evaluate side-chains 32 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.129316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.085946 restraints weight = 59429.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.082509 restraints weight = 54222.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.082256 restraints weight = 40202.461| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6729 Z= 0.171 Angle : 0.590 8.463 9156 Z= 0.306 Chirality : 0.044 0.205 1019 Planarity : 0.005 0.089 1178 Dihedral : 4.907 24.674 950 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.73 (0.28), residues: 822 helix: -3.79 (0.82), residues: 20 sheet: -0.08 (0.29), residues: 319 loop : -1.86 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.011 0.001 HIS C 66 PHE 0.012 0.001 PHE L 144 TYR 0.023 0.001 TYR L 145 ARG 0.002 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.9308 (m-80) cc_final: 0.8909 (m-80) REVERT: B 505 TYR cc_start: 0.8874 (m-80) cc_final: 0.8551 (t80) REVERT: H 102 MET cc_start: 0.2060 (ppp) cc_final: 0.1490 (mpp) REVERT: H 117 MET cc_start: 0.5757 (mmp) cc_final: 0.4933 (mmp) REVERT: L 91 TYR cc_start: 0.5806 (m-10) cc_final: 0.5441 (m-10) REVERT: L 94 MET cc_start: 0.4310 (mmp) cc_final: 0.3889 (mmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1717 time to fit residues: 9.2509 Evaluate side-chains 30 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 64 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 66 optimal weight: 0.0770 chunk 5 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** 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 = 0.4348 r_free = 0.4348 target = 0.141889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.111567 restraints weight = 62052.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.108317 restraints weight = 59357.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.108274 restraints weight = 46983.820| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6729 Z= 0.144 Angle : 0.565 7.870 9156 Z= 0.291 Chirality : 0.044 0.199 1019 Planarity : 0.005 0.091 1178 Dihedral : 4.714 23.553 950 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.69 (0.28), residues: 822 helix: -3.52 (0.63), residues: 32 sheet: 0.08 (0.29), residues: 326 loop : -1.92 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.009 0.001 HIS C 66 PHE 0.012 0.001 PHE B 497 TYR 0.013 0.001 TYR C 266 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.9188 (m-80) cc_final: 0.8833 (m-80) REVERT: H 102 MET cc_start: 0.2963 (ppp) cc_final: 0.2170 (mpp) REVERT: L 91 TYR cc_start: 0.6112 (m-10) cc_final: 0.5778 (m-10) REVERT: L 94 MET cc_start: 0.4356 (mmp) cc_final: 0.4002 (mmm) REVERT: L 178 TYR cc_start: 0.1870 (m-10) cc_final: 0.1647 (m-10) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1594 time to fit residues: 8.8793 Evaluate side-chains 27 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** 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 = 0.4283 r_free = 0.4283 target = 0.138808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.107623 restraints weight = 61920.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.105401 restraints weight = 56627.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.105082 restraints weight = 43529.195| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.8147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 6729 Z= 0.264 Angle : 0.689 7.744 9156 Z= 0.359 Chirality : 0.046 0.281 1019 Planarity : 0.006 0.098 1178 Dihedral : 5.471 30.117 950 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.82 (0.28), residues: 822 helix: -3.67 (0.70), residues: 26 sheet: -0.17 (0.29), residues: 330 loop : -1.90 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 64 HIS 0.013 0.002 HIS C 66 PHE 0.019 0.002 PHE C 186 TYR 0.027 0.002 TYR L 145 ARG 0.004 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.2754 (ppp) cc_final: 0.1961 (mpp) REVERT: L 91 TYR cc_start: 0.5734 (m-80) cc_final: 0.5414 (m-10) REVERT: L 94 MET cc_start: 0.4723 (mmp) cc_final: 0.4054 (mmm) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1500 time to fit residues: 10.0867 Evaluate side-chains 36 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** 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 = 0.4296 r_free = 0.4296 target = 0.139276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.084026 restraints weight = 62433.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.082114 restraints weight = 53356.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.082603 restraints weight = 44607.714| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.8344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6729 Z= 0.196 Angle : 0.630 7.658 9156 Z= 0.325 Chirality : 0.045 0.237 1019 Planarity : 0.005 0.099 1178 Dihedral : 5.192 25.431 950 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.89 (0.28), residues: 822 helix: -4.15 (0.63), residues: 26 sheet: -0.04 (0.29), residues: 325 loop : -2.06 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.011 0.001 HIS C 66 PHE 0.011 0.002 PHE L 144 TYR 0.022 0.002 TYR L 145 ARG 0.003 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.681 Fit side-chains REVERT: H 102 MET cc_start: 0.1573 (ppp) cc_final: 0.1027 (mpp) REVERT: H 117 MET cc_start: 0.6222 (mmp) cc_final: 0.5730 (mmp) REVERT: L 94 MET cc_start: 0.4618 (mmp) cc_final: 0.3830 (mmm) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1569 time to fit residues: 10.0103 Evaluate side-chains 32 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 48 optimal weight: 30.0000 chunk 81 optimal weight: 0.0170 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** 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 = 0.4315 r_free = 0.4315 target = 0.139943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.106136 restraints weight = 62036.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.104781 restraints weight = 61103.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.104326 restraints weight = 49161.349| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.8380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6729 Z= 0.152 Angle : 0.592 7.739 9156 Z= 0.306 Chirality : 0.045 0.161 1019 Planarity : 0.005 0.097 1178 Dihedral : 4.791 22.968 950 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.65 (0.28), residues: 822 helix: -3.84 (0.64), residues: 32 sheet: 0.16 (0.29), residues: 320 loop : -1.89 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.009 0.001 HIS C 66 PHE 0.011 0.001 PHE L 103 TYR 0.014 0.001 TYR L 145 ARG 0.003 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.2143 (ppp) cc_final: 0.1571 (mpp) REVERT: H 117 MET cc_start: 0.6426 (mmp) cc_final: 0.5986 (mmp) REVERT: L 94 MET cc_start: 0.3832 (mmp) cc_final: 0.3265 (mmt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1610 time to fit residues: 9.5353 Evaluate side-chains 31 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 481 ASN ** L 165 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 = 0.4142 r_free = 0.4142 target = 0.130670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.078408 restraints weight = 42751.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.078510 restraints weight = 35026.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.077430 restraints weight = 34377.942| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 1.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.145 6729 Z= 0.592 Angle : 1.139 14.619 9156 Z= 0.592 Chirality : 0.061 0.448 1019 Planarity : 0.008 0.114 1178 Dihedral : 7.910 31.357 950 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 42.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.63 (0.27), residues: 822 helix: -4.26 (0.44), residues: 30 sheet: -0.56 (0.29), residues: 316 loop : -2.53 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP H 171 HIS 0.018 0.003 HIS C 66 PHE 0.041 0.005 PHE C 192 TYR 0.058 0.004 TYR L 145 ARG 0.014 0.002 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4165.33 seconds wall clock time: 74 minutes 18.11 seconds (4458.11 seconds total)