Starting phenix.real_space_refine on Thu Jul 2 04:42:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f46_31444/07_2026/7f46_31444.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f46_31444/07_2026/7f46_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 { model { file = "/net/cci-nas-00/data/ceres_data/7f46_31444/07_2026/7f46_31444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f46_31444/07_2026/7f46_31444.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7f46_31444/07_2026/7f46_31444.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f46_31444/07_2026/7f46_31444.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f46_31444/07_2026/7f46_31444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f46_31444/07_2026/7f46_31444.map" } 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-dev-6108/lib/python3.11/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 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 chiralities: 1 Time building chain proxies: 1.09, per 1000 atoms: 0.17 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: 0.42 Conformation dependent library (CDL) restraints added in 265.3 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: 0.11 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: 0.66 Time building geometry restraints manager: 0.61 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: 3540 17.08 - 34.15: 343 34.15 - 51.23: 54 51.23 - 68.31: 10 68.31 - 85.38: 3 Dihedral angle restraints: 3950 sinusoidal: 1517 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 3947 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: 2.540 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 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 : 13.378 85.382 2370 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 are 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/Z covalent geometry : bond 0.00584 / 0.35 ( 6729) covalent geometry : angle 0.84030 / 0.51 ( 9156) SS BOND : bond 0.00545 / 0.40 ( 8) SS BOND : angle 1.10280 / 0.65 ( 16) hydrogen bonds : bond 0.12061 / 7.90 ( 221) hydrogen bonds : angle 6.76126 / 4.60 ( 546) link_NAG-ASN : bond 0.00684 / 0.35 ( 2) link_NAG-ASN : angle 3.72883 / 2.24 ( 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 : 0.150 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: 0.0496 time to fit residues: 5.3786 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 : 0.144 ------------------------------------------------------------------------------- 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... C 207 HIS ** B 422 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.138692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.080969 restraints weight = 37441.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.080400 restraints weight = 33039.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.080346 restraints weight = 30619.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.080835 restraints weight = 28600.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.079179 restraints weight = 26368.463| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 6739 Z= 0.298 Angle : 0.917 10.884 9178 Z= 0.480 Chirality : 0.051 0.203 1019 Planarity : 0.007 0.106 1178 Dihedral : 6.531 27.949 908 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.69 % Allowed : 9.93 % Favored : 89.38 % 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 are not related in a simple way. whole: -2.78 (0.27), residues: 822 helix: -4.23 (0.54), residues: 31 sheet: -0.72 (0.29), residues: 318 loop : -2.60 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 19 TYR 0.036 0.003 TYR L 145 PHE 0.026 0.003 PHE L 121 TRP 0.042 0.003 TRP H 53 HIS 0.010 0.003 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.30 ( 6729) covalent geometry : angle 0.91348 / 0.48 ( 9156) SS BOND : bond 0.00815 / 0.60 ( 8) SS BOND : angle 1.99656 / 1.19 ( 16) hydrogen bonds : bond 0.05608 / 3.95 ( 221) hydrogen bonds : angle 7.09422 / 4.85 ( 546) link_NAG-ASN : bond 0.00500 / 0.25 ( 2) link_NAG-ASN : angle 1.77541 / 1.00 ( 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: 5 poor density : 55 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8468 (mm) REVERT: H 102 MET cc_start: 0.1294 (ppp) cc_final: 0.0880 (mpp) REVERT: H 155 LEU cc_start: -0.6778 (OUTLIER) cc_final: -0.7720 (mp) REVERT: L 53 ILE cc_start: 0.3015 (mt) cc_final: 0.2020 (mt) REVERT: L 77 THR cc_start: 0.4220 (p) cc_final: 0.3991 (p) REVERT: L 94 MET cc_start: 0.8057 (ttt) cc_final: 0.7456 (tmm) outliers start: 5 outliers final: 1 residues processed: 60 average time/residue: 0.0684 time to fit residues: 6.1147 Evaluate side-chains 37 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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: 0.0770 chunk 42 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 30 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.142219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.113114 restraints weight = 62662.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.109405 restraints weight = 58169.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.109471 restraints weight = 46752.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.108748 restraints weight = 40041.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.108631 restraints weight = 37150.785| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6739 Z= 0.193 Angle : 0.736 10.311 9178 Z= 0.382 Chirality : 0.048 0.269 1019 Planarity : 0.006 0.087 1178 Dihedral : 5.748 24.882 908 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % 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 are not related in a simple way. whole: -2.48 (0.28), residues: 822 helix: -3.88 (0.68), residues: 25 sheet: -0.80 (0.28), residues: 335 loop : -2.23 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 408 TYR 0.032 0.002 TYR L 145 PHE 0.017 0.002 PHE C 140 TRP 0.013 0.002 TRP C 64 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 ( 6729) covalent geometry : angle 0.72909 / 0.38 ( 9156) SS BOND : bond 0.00963 / 0.72 ( 8) SS BOND : angle 1.96168 / 1.16 ( 16) hydrogen bonds : bond 0.04040 / 2.82 ( 221) hydrogen bonds : angle 6.48342 / 4.49 ( 546) link_NAG-ASN : bond 0.00654 / 0.31 ( 2) link_NAG-ASN : angle 2.57090 / 1.57 ( 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 : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.2893 (ppp) cc_final: 0.2136 (mpp) REVERT: L 178 TYR cc_start: 0.0261 (m-80) cc_final: -0.0160 (m-80) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.0595 time to fit residues: 4.1708 Evaluate side-chains 34 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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: 5.9990 chunk 63 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS L 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.138167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.081482 restraints weight = 37605.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.080874 restraints weight = 29231.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.080900 restraints weight = 26270.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.080900 restraints weight = 25388.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.080900 restraints weight = 25388.853| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 6739 Z= 0.195 Angle : 0.720 9.612 9178 Z= 0.374 Chirality : 0.047 0.288 1019 Planarity : 0.006 0.094 1178 Dihedral : 5.747 24.097 908 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.28), residues: 822 helix: -3.76 (0.89), residues: 19 sheet: -0.68 (0.29), residues: 327 loop : -2.20 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 214 TYR 0.032 0.002 TYR C 266 PHE 0.016 0.002 PHE C 186 TRP 0.022 0.002 TRP C 64 HIS 0.020 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 ( 6729) covalent geometry : angle 0.71594 / 0.37 ( 9156) SS BOND : bond 0.01442 / 1.09 ( 8) SS BOND : angle 1.50060 / 0.85 ( 16) hydrogen bonds : bond 0.03995 / 2.71 ( 221) hydrogen bonds : angle 6.64785 / 4.65 ( 546) link_NAG-ASN : bond 0.00210 / 0.10 ( 2) link_NAG-ASN : angle 1.97171 / 1.21 ( 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 43 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 505 TYR cc_start: 0.9024 (m-80) cc_final: 0.8588 (t80) REVERT: H 102 MET cc_start: 0.2450 (ppp) cc_final: 0.1823 (mpp) REVERT: L 91 TYR cc_start: 0.5271 (m-10) cc_final: 0.4922 (m-10) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0703 time to fit residues: 4.4805 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 : 0.354 ------------------------------------------------------------------------------- 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: 8.9990 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 chunk 74 optimal weight: 6.9990 chunk 40 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4307 r_free = 0.4307 target = 0.141307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.083266 restraints weight = 63756.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.081319 restraints weight = 51849.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.081733 restraints weight = 42973.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.082180 restraints weight = 38763.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.082180 restraints weight = 34936.042| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6739 Z= 0.137 Angle : 0.641 7.824 9178 Z= 0.332 Chirality : 0.045 0.217 1019 Planarity : 0.005 0.092 1178 Dihedral : 5.313 22.787 908 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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 are not related in a simple way. whole: -2.27 (0.28), residues: 822 helix: -3.91 (0.68), residues: 25 sheet: -0.46 (0.29), residues: 324 loop : -2.22 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 214 TYR 0.020 0.001 TYR L 145 PHE 0.014 0.002 PHE L 144 TRP 0.015 0.001 TRP C 64 HIS 0.015 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 6729) covalent geometry : angle 0.63640 / 0.33 ( 9156) SS BOND : bond 0.00710 / 0.53 ( 8) SS BOND : angle 1.73716 / 1.00 ( 16) hydrogen bonds : bond 0.03283 / 2.23 ( 221) hydrogen bonds : angle 6.21465 / 4.39 ( 546) link_NAG-ASN : bond 0.00219 / 0.11 ( 2) link_NAG-ASN : angle 1.41597 / 0.89 ( 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 41 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 277 LEU cc_start: 0.9545 (mp) cc_final: 0.9020 (tt) REVERT: H 102 MET cc_start: 0.1475 (ppp) cc_final: 0.0952 (mpp) REVERT: H 117 MET cc_start: 0.6716 (mmp) cc_final: 0.6369 (mmp) REVERT: L 91 TYR cc_start: 0.5560 (m-10) cc_final: 0.5228 (m-10) REVERT: L 94 MET cc_start: 0.4186 (mmm) cc_final: 0.3754 (mmt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0754 time to fit residues: 4.5279 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 : 0.251 ------------------------------------------------------------------------------- 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: 7.9990 chunk 39 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS L 50 GLN L 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.141106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.079949 restraints weight = 63607.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.078289 restraints weight = 49707.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.077944 restraints weight = 41628.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.078011 restraints weight = 37923.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.078019 restraints weight = 37101.682| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.7276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6739 Z= 0.109 Angle : 0.591 7.034 9178 Z= 0.305 Chirality : 0.044 0.179 1019 Planarity : 0.005 0.090 1178 Dihedral : 4.921 21.323 908 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % 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 are not related in a simple way. whole: -1.98 (0.28), residues: 822 helix: -3.89 (0.71), residues: 25 sheet: -0.20 (0.29), residues: 322 loop : -2.06 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.016 0.001 TYR C 266 PHE 0.014 0.001 PHE L 144 TRP 0.014 0.001 TRP C 64 HIS 0.012 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6729) covalent geometry : angle 0.58856 / 0.30 ( 9156) SS BOND : bond 0.00585 / 0.44 ( 8) SS BOND : angle 1.17522 / 0.62 ( 16) hydrogen bonds : bond 0.02936 / 1.97 ( 221) hydrogen bonds : angle 5.88605 / 4.18 ( 546) link_NAG-ASN : bond 0.00230 / 0.11 ( 2) link_NAG-ASN : angle 1.21438 / 0.76 ( 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 42 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.251 Fit side-chains REVERT: C 277 LEU cc_start: 0.9513 (mp) cc_final: 0.9015 (tt) REVERT: B 505 TYR cc_start: 0.9230 (m-80) cc_final: 0.8710 (t80) REVERT: H 102 MET cc_start: 0.1494 (ppp) cc_final: 0.0959 (mpp) REVERT: H 117 MET cc_start: 0.6156 (mmp) cc_final: 0.5840 (mmp) REVERT: L 91 TYR cc_start: 0.5647 (m-10) cc_final: 0.5347 (m-10) REVERT: L 94 MET cc_start: 0.4378 (mmm) cc_final: 0.3828 (mmt) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0646 time to fit residues: 4.1036 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 : 0.184 ------------------------------------------------------------------------------- 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: 5.9990 chunk 80 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.139414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.107527 restraints weight = 61905.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.104684 restraints weight = 59374.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.104211 restraints weight = 43949.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.104973 restraints weight = 35494.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.104655 restraints weight = 26624.840| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.7966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6739 Z= 0.158 Angle : 0.655 7.554 9178 Z= 0.341 Chirality : 0.046 0.251 1019 Planarity : 0.005 0.095 1178 Dihedral : 5.190 22.342 908 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.28), residues: 822 helix: -3.86 (0.70), residues: 25 sheet: -0.24 (0.29), residues: 329 loop : -2.06 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.024 0.002 TYR L 145 PHE 0.015 0.002 PHE C 186 TRP 0.013 0.002 TRP C 64 HIS 0.011 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 6729) covalent geometry : angle 0.65195 / 0.34 ( 9156) SS BOND : bond 0.00671 / 0.50 ( 8) SS BOND : angle 1.54289 / 0.90 ( 16) hydrogen bonds : bond 0.03384 / 2.31 ( 221) hydrogen bonds : angle 6.19925 / 4.39 ( 546) link_NAG-ASN : bond 0.00203 / 0.10 ( 2) link_NAG-ASN : angle 1.17014 / 0.77 ( 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 48 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.256 Fit side-chains REVERT: C 277 LEU cc_start: 0.9559 (mp) cc_final: 0.9059 (tt) REVERT: B 505 TYR cc_start: 0.8911 (m-80) cc_final: 0.8577 (t80) REVERT: H 102 MET cc_start: 0.2947 (ppp) cc_final: 0.2237 (mpp) REVERT: H 117 MET cc_start: 0.6427 (mmp) cc_final: 0.6014 (mmp) REVERT: L 91 TYR cc_start: 0.5749 (m-80) cc_final: 0.5494 (m-10) REVERT: L 94 MET cc_start: 0.5123 (mmm) cc_final: 0.4405 (mmt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0553 time to fit residues: 4.1305 Evaluate side-chains 34 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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: 0.0070 chunk 1 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.127791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.090591 restraints weight = 62723.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.088316 restraints weight = 60035.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.088903 restraints weight = 42430.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.088236 restraints weight = 37608.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.088238 restraints weight = 33038.880| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.8261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6739 Z= 0.129 Angle : 0.630 8.690 9178 Z= 0.324 Chirality : 0.045 0.203 1019 Planarity : 0.005 0.095 1178 Dihedral : 5.025 20.972 908 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.28), residues: 822 helix: -3.36 (0.87), residues: 24 sheet: -0.13 (0.29), residues: 324 loop : -2.07 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 408 TYR 0.020 0.001 TYR L 145 PHE 0.012 0.001 PHE L 144 TRP 0.013 0.001 TRP C 64 HIS 0.011 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6729) covalent geometry : angle 0.62796 / 0.32 ( 9156) SS BOND : bond 0.00620 / 0.47 ( 8) SS BOND : angle 1.28683 / 0.75 ( 16) hydrogen bonds : bond 0.03054 / 2.07 ( 221) hydrogen bonds : angle 6.00029 / 4.26 ( 546) link_NAG-ASN : bond 0.00206 / 0.10 ( 2) link_NAG-ASN : angle 1.19962 / 0.77 ( 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 43 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.267 Fit side-chains REVERT: C 277 LEU cc_start: 0.9509 (mp) cc_final: 0.9075 (tt) REVERT: B 505 TYR cc_start: 0.8889 (m-80) cc_final: 0.8563 (t80) REVERT: H 102 MET cc_start: 0.2373 (ppp) cc_final: 0.1838 (mpp) REVERT: H 117 MET cc_start: 0.6121 (mmp) cc_final: 0.5660 (mmp) REVERT: L 94 MET cc_start: 0.5044 (mmm) cc_final: 0.4823 (mmt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0629 time to fit residues: 4.2266 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 : 0.252 ------------------------------------------------------------------------------- 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: 1.9990 chunk 67 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.137266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.103581 restraints weight = 62619.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.100619 restraints weight = 61814.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.101416 restraints weight = 43533.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.100605 restraints weight = 38891.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.100536 restraints weight = 40706.658| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.9078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 6739 Z= 0.213 Angle : 0.750 7.861 9178 Z= 0.391 Chirality : 0.048 0.303 1019 Planarity : 0.006 0.101 1178 Dihedral : 5.659 22.318 908 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.28), residues: 822 helix: -3.89 (0.66), residues: 30 sheet: -0.24 (0.29), residues: 331 loop : -2.23 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 104 TYR 0.027 0.002 TYR L 145 PHE 0.025 0.002 PHE C 186 TRP 0.012 0.002 TRP H 171 HIS 0.012 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 6729) covalent geometry : angle 0.74492 / 0.39 ( 9156) SS BOND : bond 0.00736 / 0.54 ( 8) SS BOND : angle 1.96238 / 1.14 ( 16) hydrogen bonds : bond 0.03802 / 2.58 ( 221) hydrogen bonds : angle 6.66263 / 4.70 ( 546) link_NAG-ASN : bond 0.00078 / 0.04 ( 2) link_NAG-ASN : angle 1.88310 / 1.18 ( 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 40 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.258 Fit side-chains REVERT: B 505 TYR cc_start: 0.8871 (m-80) cc_final: 0.8507 (t80) REVERT: H 102 MET cc_start: 0.2200 (ppp) cc_final: 0.1685 (mpp) REVERT: H 117 MET cc_start: 0.5957 (mmp) cc_final: 0.5586 (mmp) REVERT: L 94 MET cc_start: 0.5294 (mmm) cc_final: 0.4983 (mmt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0571 time to fit residues: 3.7738 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 : 0.256 ------------------------------------------------------------------------------- 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: 4.9990 chunk 64 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 66 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.138192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.109873 restraints weight = 62245.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.106582 restraints weight = 61718.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.106821 restraints weight = 43787.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.106583 restraints weight = 32333.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.106654 restraints weight = 25988.593| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.9114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6739 Z= 0.136 Angle : 0.663 7.430 9178 Z= 0.343 Chirality : 0.046 0.206 1019 Planarity : 0.005 0.101 1178 Dihedral : 5.269 20.423 908 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % 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 are not related in a simple way. whole: -2.01 (0.28), residues: 822 helix: -3.91 (0.80), residues: 24 sheet: -0.11 (0.29), residues: 324 loop : -2.19 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.018 0.001 TYR L 145 PHE 0.022 0.002 PHE B 400 TRP 0.012 0.001 TRP C 64 HIS 0.011 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 6729) covalent geometry : angle 0.66074 / 0.34 ( 9156) SS BOND : bond 0.00592 / 0.44 ( 8) SS BOND : angle 1.22181 / 0.69 ( 16) hydrogen bonds : bond 0.03128 / 2.10 ( 221) hydrogen bonds : angle 6.26852 / 4.42 ( 546) link_NAG-ASN : bond 0.00194 / 0.10 ( 2) link_NAG-ASN : angle 1.35731 / 0.85 ( 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 41 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.281 Fit side-chains REVERT: C 277 LEU cc_start: 0.9500 (mp) cc_final: 0.9070 (tt) REVERT: B 505 TYR cc_start: 0.8807 (m-80) cc_final: 0.8538 (t80) REVERT: H 102 MET cc_start: 0.3138 (ppp) cc_final: 0.2280 (mpp) REVERT: H 117 MET cc_start: 0.6063 (mmp) cc_final: 0.5656 (mmp) REVERT: L 91 TYR cc_start: 0.5319 (m-80) cc_final: 0.5014 (m-10) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0546 time to fit residues: 3.6521 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 : 0.248 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.137595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.108442 restraints weight = 62203.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.105110 restraints weight = 59280.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.105279 restraints weight = 44514.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.105392 restraints weight = 32555.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.105189 restraints weight = 26186.601| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.9379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6739 Z= 0.136 Angle : 0.656 7.417 9178 Z= 0.340 Chirality : 0.046 0.195 1019 Planarity : 0.005 0.100 1178 Dihedral : 5.226 20.452 908 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.28), residues: 822 helix: -3.76 (0.88), residues: 24 sheet: -0.02 (0.29), residues: 326 loop : -2.13 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.036 0.002 TYR L 41 PHE 0.012 0.001 PHE C 186 TRP 0.012 0.001 TRP C 64 HIS 0.010 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 6729) covalent geometry : angle 0.65381 / 0.34 ( 9156) SS BOND : bond 0.00577 / 0.43 ( 8) SS BOND : angle 1.28304 / 0.74 ( 16) hydrogen bonds : bond 0.03143 / 2.14 ( 221) hydrogen bonds : angle 6.16050 / 4.35 ( 546) link_NAG-ASN : bond 0.00190 / 0.09 ( 2) link_NAG-ASN : angle 1.32183 / 0.83 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2597.61 seconds wall clock time: 45 minutes 12.61 seconds (2712.61 seconds total)