Starting phenix.real_space_refine on Fri Aug 22 18:10:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f46_31444/08_2025/7f46_31444.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f46_31444/08_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_31444/08_2025/7f46_31444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f46_31444/08_2025/7f46_31444.map" model { file = "/net/cci-nas-00/data/ceres_data/7f46_31444/08_2025/7f46_31444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f46_31444/08_2025/7f46_31444.cif" } resolution = 4.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.44, per 1000 atoms: 0.22 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: 0.39 Conformation dependent library (CDL) restraints added in 252.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.22 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: 0.76 Time building geometry restraints manager: 0.54 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.930 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.300 ------------------------------------------------------------------------------- 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 6739 Z= 0.349 Angle : 0.846 7.883 9178 Z= 0.508 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (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 ARG 0.005 0.001 ARG B 408 TYR 0.034 0.002 TYR B 473 PHE 0.020 0.002 PHE H 139 TRP 0.016 0.002 TRP B 436 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 6729) covalent geometry : angle 0.84030 ( 9156) SS BOND : bond 0.00545 ( 8) SS BOND : angle 1.10280 ( 16) hydrogen bonds : bond 0.12061 ( 221) hydrogen bonds : angle 6.76126 ( 546) link_NAG-ASN : bond 0.00684 ( 2) link_NAG-ASN : angle 3.72883 ( 6) *********************** 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 : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.8147 (m-30) cc_final: 0.7907 (m-30) REVERT: H 102 MET cc_start: 0.0415 (ppp) cc_final: -0.0070 (mpp) REVERT: H 117 MET cc_start: 0.6580 (mtt) cc_final: 0.5379 (mmp) REVERT: H 198 VAL cc_start: 0.1912 (p) cc_final: 0.1365 (t) REVERT: L 41 TYR cc_start: 0.6811 (m-80) cc_final: 0.6400 (m-80) REVERT: L 91 TYR cc_start: 0.6202 (m-10) cc_final: 0.5714 (m-10) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0561 time to fit residues: 6.0242 Evaluate side-chains 41 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN C 207 HIS ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** 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 = 0.4272 r_free = 0.4272 target = 0.137200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.079718 restraints weight = 37922.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.077843 restraints weight = 28576.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.077843 restraints weight = 23192.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.077843 restraints weight = 23192.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.077843 restraints weight = 23192.680| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 6739 Z= 0.313 Angle : 0.959 11.379 9178 Z= 0.504 Chirality : 0.053 0.323 1019 Planarity : 0.008 0.103 1178 Dihedral : 7.404 40.237 950 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.97 % Allowed : 11.31 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.27), residues: 822 helix: -4.27 (0.53), residues: 31 sheet: -0.80 (0.29), residues: 315 loop : -2.63 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 408 TYR 0.043 0.004 TYR L 145 PHE 0.027 0.003 PHE L 121 TRP 0.048 0.004 TRP H 53 HIS 0.008 0.002 HIS H 217 Details of bonding type rmsd covalent geometry : bond 0.00672 ( 6729) covalent geometry : angle 0.95495 ( 9156) SS BOND : bond 0.00851 ( 8) SS BOND : angle 1.98392 ( 16) hydrogen bonds : bond 0.05930 ( 221) hydrogen bonds : angle 7.31811 ( 546) link_NAG-ASN : bond 0.00683 ( 2) link_NAG-ASN : angle 2.37496 ( 6) *********************** 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 60 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8911 (p0) REVERT: H 102 MET cc_start: 0.1403 (ppp) cc_final: 0.1113 (mpp) REVERT: H 155 LEU cc_start: -0.6623 (OUTLIER) cc_final: -0.7509 (mp) REVERT: L 53 ILE cc_start: 0.3036 (mt) cc_final: 0.2174 (mt) REVERT: L 77 THR cc_start: 0.4250 (p) cc_final: 0.4026 (p) outliers start: 7 outliers final: 1 residues processed: 60 average time/residue: 0.0588 time to fit residues: 5.2315 Evaluate side-chains 34 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.0370 overall best weight: 2.3464 ------------------------------------------------------------------------------- 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 481 ASN L 31 HIS L 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.141306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.081544 restraints weight = 62542.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.080980 restraints weight = 49332.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.079641 restraints weight = 42012.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.079903 restraints weight = 36612.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.079903 restraints weight = 33959.312| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 6739 Z= 0.223 Angle : 0.776 10.490 9178 Z= 0.403 Chirality : 0.049 0.294 1019 Planarity : 0.006 0.092 1178 Dihedral : 6.438 41.253 950 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.14 % Allowed : 5.79 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.27), residues: 822 helix: -3.89 (0.77), residues: 19 sheet: -0.81 (0.28), residues: 329 loop : -2.43 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 214 TYR 0.035 0.002 TYR L 145 PHE 0.018 0.002 PHE C 140 TRP 0.013 0.002 TRP C 64 HIS 0.010 0.002 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 6729) covalent geometry : angle 0.76728 ( 9156) SS BOND : bond 0.00994 ( 8) SS BOND : angle 2.19975 ( 16) hydrogen bonds : bond 0.04362 ( 221) hydrogen bonds : angle 6.80190 ( 546) link_NAG-ASN : bond 0.00743 ( 2) link_NAG-ASN : angle 2.94410 ( 6) *********************** 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 46 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.1322 (ppp) cc_final: 0.1044 (mpp) REVERT: L 178 TYR cc_start: 0.0033 (m-80) cc_final: -0.0232 (m-10) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.0628 time to fit residues: 4.1731 Evaluate side-chains 33 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 8.9990 chunk 63 optimal weight: 30.0000 chunk 45 optimal weight: 0.0570 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- 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** L 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.142422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.101071 restraints weight = 62853.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.095542 restraints weight = 56497.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.095372 restraints weight = 43259.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.095019 restraints weight = 35196.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.095175 restraints weight = 30148.031| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6739 Z= 0.127 Angle : 0.636 7.525 9178 Z= 0.331 Chirality : 0.045 0.208 1019 Planarity : 0.005 0.093 1178 Dihedral : 5.421 25.582 950 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.28), residues: 822 helix: -3.60 (0.75), residues: 25 sheet: -0.67 (0.28), residues: 328 loop : -2.20 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.024 0.001 TYR C 266 PHE 0.014 0.001 PHE L 144 TRP 0.019 0.002 TRP C 64 HIS 0.020 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6729) covalent geometry : angle 0.63323 ( 9156) SS BOND : bond 0.00679 ( 8) SS BOND : angle 1.20826 ( 16) hydrogen bonds : bond 0.03378 ( 221) hydrogen bonds : angle 6.28866 ( 546) link_NAG-ASN : bond 0.00241 ( 2) link_NAG-ASN : angle 1.64892 ( 6) *********************** 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 39 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 505 TYR cc_start: 0.8921 (m-80) cc_final: 0.8575 (t80) REVERT: H 102 MET cc_start: 0.1349 (ppp) cc_final: 0.1122 (mpp) REVERT: L 91 TYR cc_start: 0.5299 (m-10) cc_final: 0.4934 (m-10) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0707 time to fit residues: 4.1120 Evaluate side-chains 28 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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 481 ASN H 82 HIS ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.133830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.081634 restraints weight = 41327.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.081125 restraints weight = 34902.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.081265 restraints weight = 31884.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.079578 restraints weight = 37957.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.079472 restraints weight = 36573.406| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.8823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.149 6739 Z= 0.334 Angle : 0.961 12.825 9178 Z= 0.501 Chirality : 0.054 0.397 1019 Planarity : 0.008 0.101 1178 Dihedral : 7.340 32.536 950 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 34.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.28 % Allowed : 6.48 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.27), residues: 822 helix: -3.99 (0.59), residues: 25 sheet: -0.95 (0.28), residues: 335 loop : -2.52 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 457 TYR 0.032 0.004 TYR L 145 PHE 0.034 0.004 PHE C 186 TRP 0.025 0.003 TRP H 171 HIS 0.016 0.003 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00748 ( 6729) covalent geometry : angle 0.95301 ( 9156) SS BOND : bond 0.00767 ( 8) SS BOND : angle 2.62015 ( 16) hydrogen bonds : bond 0.05466 ( 221) hydrogen bonds : angle 8.27261 ( 546) link_NAG-ASN : bond 0.00356 ( 2) link_NAG-ASN : angle 2.75628 ( 6) *********************** 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 43 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.2316 (ppp) cc_final: 0.1998 (ptp) REVERT: L 94 MET cc_start: 0.4103 (mmt) cc_final: 0.3683 (mmt) REVERT: L 171 GLN cc_start: -0.0660 (OUTLIER) cc_final: -0.0931 (tt0) outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 0.0582 time to fit residues: 3.7971 Evaluate side-chains 31 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.139364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.098587 restraints weight = 62945.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.096095 restraints weight = 55836.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095969 restraints weight = 44636.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.096075 restraints weight = 38742.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.095597 restraints weight = 39870.508| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.8487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6739 Z= 0.142 Angle : 0.678 8.008 9178 Z= 0.354 Chirality : 0.047 0.221 1019 Planarity : 0.006 0.097 1178 Dihedral : 5.871 26.235 950 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.27), residues: 822 helix: -3.82 (0.63), residues: 25 sheet: -0.46 (0.29), residues: 323 loop : -2.42 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 59 TYR 0.020 0.002 TYR L 145 PHE 0.013 0.002 PHE L 144 TRP 0.015 0.002 TRP H 171 HIS 0.013 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6729) covalent geometry : angle 0.67536 ( 9156) SS BOND : bond 0.00656 ( 8) SS BOND : angle 1.51395 ( 16) hydrogen bonds : bond 0.03392 ( 221) hydrogen bonds : angle 6.73415 ( 546) link_NAG-ASN : bond 0.00070 ( 2) link_NAG-ASN : angle 1.20113 ( 6) *********************** 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 47 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.1702 (ppp) cc_final: 0.1460 (ptp) REVERT: L 53 ILE cc_start: 0.4082 (mt) cc_final: 0.3831 (mt) REVERT: L 91 TYR cc_start: 0.5259 (m-80) cc_final: 0.5018 (m-10) REVERT: L 94 MET cc_start: 0.4085 (mmt) cc_final: 0.3620 (mmt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0641 time to fit residues: 4.3653 Evaluate side-chains 35 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.136389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.099425 restraints weight = 62021.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.095887 restraints weight = 61132.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.096193 restraints weight = 47672.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.095093 restraints weight = 38945.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.095040 restraints weight = 35619.915| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.9503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 6739 Z= 0.248 Angle : 0.805 8.425 9178 Z= 0.423 Chirality : 0.050 0.274 1019 Planarity : 0.007 0.104 1178 Dihedral : 6.481 30.935 950 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.27), residues: 822 helix: -3.75 (0.62), residues: 30 sheet: -0.58 (0.28), residues: 331 loop : -2.48 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 104 TYR 0.034 0.003 TYR L 145 PHE 0.025 0.003 PHE C 186 TRP 0.013 0.002 TRP C 64 HIS 0.012 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 6729) covalent geometry : angle 0.79976 ( 9156) SS BOND : bond 0.00624 ( 8) SS BOND : angle 2.03674 ( 16) hydrogen bonds : bond 0.04326 ( 221) hydrogen bonds : angle 7.52609 ( 546) link_NAG-ASN : bond 0.00313 ( 2) link_NAG-ASN : angle 1.72851 ( 6) *********************** 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 43 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.2494 (ppp) cc_final: 0.2148 (ptp) REVERT: L 94 MET cc_start: 0.4412 (mmt) cc_final: 0.4088 (mmt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0660 time to fit residues: 4.2778 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 : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 45 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** H 172 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 = 0.4264 r_free = 0.4264 target = 0.138279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.089348 restraints weight = 62540.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.088074 restraints weight = 56853.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.087713 restraints weight = 48166.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.087869 restraints weight = 42715.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.087571 restraints weight = 42962.575| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.9447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6739 Z= 0.136 Angle : 0.668 7.992 9178 Z= 0.351 Chirality : 0.047 0.217 1019 Planarity : 0.006 0.103 1178 Dihedral : 5.757 25.140 950 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.28), residues: 822 helix: -3.61 (0.66), residues: 31 sheet: -0.25 (0.29), residues: 314 loop : -2.41 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.018 0.002 TYR L 145 PHE 0.013 0.002 PHE L 144 TRP 0.014 0.001 TRP C 64 HIS 0.010 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6729) covalent geometry : angle 0.66579 ( 9156) SS BOND : bond 0.00503 ( 8) SS BOND : angle 1.42790 ( 16) hydrogen bonds : bond 0.03307 ( 221) hydrogen bonds : angle 6.68993 ( 546) link_NAG-ASN : bond 0.00164 ( 2) link_NAG-ASN : angle 1.18925 ( 6) *********************** 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 : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.2406 (ppp) cc_final: 0.2075 (ptp) REVERT: L 91 TYR cc_start: 0.5447 (m-10) cc_final: 0.5166 (m-10) REVERT: L 94 MET cc_start: 0.4569 (mmt) cc_final: 0.4294 (mmt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0475 time to fit residues: 3.3160 Evaluate side-chains 35 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 52 optimal weight: 0.0370 chunk 67 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 46 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.7862 ------------------------------------------------------------------------------- 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** ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.136585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.103096 restraints weight = 62606.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.100388 restraints weight = 57403.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.099703 restraints weight = 53326.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.099625 restraints weight = 42089.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.099436 restraints weight = 39665.530| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 1.0012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6739 Z= 0.180 Angle : 0.726 9.272 9178 Z= 0.379 Chirality : 0.047 0.278 1019 Planarity : 0.006 0.106 1178 Dihedral : 6.066 29.068 950 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.28), residues: 822 helix: -3.93 (0.73), residues: 18 sheet: -0.40 (0.29), residues: 324 loop : -2.38 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 104 TYR 0.023 0.002 TYR L 145 PHE 0.016 0.002 PHE C 186 TRP 0.027 0.002 TRP H 171 HIS 0.010 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6729) covalent geometry : angle 0.72240 ( 9156) SS BOND : bond 0.00620 ( 8) SS BOND : angle 1.70088 ( 16) hydrogen bonds : bond 0.03648 ( 221) hydrogen bonds : angle 7.00539 ( 546) link_NAG-ASN : bond 0.00165 ( 2) link_NAG-ASN : angle 1.64497 ( 6) *********************** 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 : 0.170 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.2833 (ppp) cc_final: 0.2501 (ptp) REVERT: L 91 TYR cc_start: 0.5009 (m-10) cc_final: 0.4723 (m-10) REVERT: L 94 MET cc_start: 0.4163 (mmt) cc_final: 0.3949 (mmt) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0506 time to fit residues: 3.3557 Evaluate side-chains 35 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** ** H 172 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 = 0.4248 r_free = 0.4248 target = 0.137160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.104144 restraints weight = 62228.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.102102 restraints weight = 54852.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.100921 restraints weight = 49590.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.101209 restraints weight = 40633.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.101033 restraints weight = 35631.653| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 1.0148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6739 Z= 0.147 Angle : 0.683 8.293 9178 Z= 0.358 Chirality : 0.046 0.211 1019 Planarity : 0.006 0.105 1178 Dihedral : 5.743 23.240 950 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.28), residues: 822 helix: -3.39 (0.62), residues: 36 sheet: -0.30 (0.29), residues: 320 loop : -2.35 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.018 0.002 TYR L 145 PHE 0.015 0.002 PHE L 103 TRP 0.013 0.002 TRP C 64 HIS 0.008 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6729) covalent geometry : angle 0.68044 ( 9156) SS BOND : bond 0.00531 ( 8) SS BOND : angle 1.48048 ( 16) hydrogen bonds : bond 0.03333 ( 221) hydrogen bonds : angle 6.63614 ( 546) link_NAG-ASN : bond 0.00155 ( 2) link_NAG-ASN : angle 1.46326 ( 6) ********************** 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 45 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.2691 (ppp) cc_final: 0.2350 (ptp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0540 time to fit residues: 3.7834 Evaluate side-chains 33 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 506 GLN ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.137121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.108514 restraints weight = 62294.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.104955 restraints weight = 56248.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.105063 restraints weight = 45829.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.105086 restraints weight = 35730.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105314 restraints weight = 32272.857| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 1.0264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6739 Z= 0.131 Angle : 0.658 8.388 9178 Z= 0.346 Chirality : 0.046 0.183 1019 Planarity : 0.006 0.103 1178 Dihedral : 5.443 28.079 950 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.28), residues: 822 helix: -3.37 (0.63), residues: 36 sheet: -0.13 (0.29), residues: 318 loop : -2.21 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.036 0.002 TYR L 41 PHE 0.011 0.001 PHE L 144 TRP 0.015 0.002 TRP H 120 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6729) covalent geometry : angle 0.65579 ( 9156) SS BOND : bond 0.00526 ( 8) SS BOND : angle 1.32880 ( 16) hydrogen bonds : bond 0.03233 ( 221) hydrogen bonds : angle 6.33213 ( 546) link_NAG-ASN : bond 0.00212 ( 2) link_NAG-ASN : angle 1.41528 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2616.16 seconds wall clock time: 45 minutes 10.86 seconds (2710.86 seconds total)