Starting phenix.real_space_refine on Wed Jul 1 23:19:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rnn_24580/07_2026/7rnn_24580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rnn_24580/07_2026/7rnn_24580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rnn_24580/07_2026/7rnn_24580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rnn_24580/07_2026/7rnn_24580.map" model { file = "/net/cci-nas-00/data/ceres_data/7rnn_24580/07_2026/7rnn_24580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rnn_24580/07_2026/7rnn_24580.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rnn_24580/07_2026/7rnn_24580.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rnn_24580/07_2026/7rnn_24580.cif" } resolution = 2.86 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= 0.000 sd= 0.001 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 30 5.16 5 C 2551 2.51 5 N 678 2.21 5 O 741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 4000 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 754 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3218 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 405} Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 116 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.07, per 1000 atoms: 0.27 Number of scatterers: 4000 At special positions: 0 Unit cell: (95.45, 60.59, 126.16, 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 30 16.00 O 741 8.00 N 678 7.00 C 2551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 179 " distance=2.05 Simple disulfide: pdb=" SG CYS D 290 " - pdb=" SG CYS D 367 " distance=2.02 Simple disulfide: pdb=" SG CYS D 310 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 314 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 323 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 325 " - pdb=" SG CYS D 337 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 3984 O5 NAG D 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG D 601 " - " ASN D 368 " " NAG D 602 " - " ASN D 395 " Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 160.6 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 7 sheets defined 32.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'D' and resid 40 through 71 removed outlier: 3.813A pdb=" N ALA D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU D 63 " --> pdb=" O CYS D 59 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 153 through 162 Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 225 through 229 removed outlier: 3.625A pdb=" N TYR D 229 " --> pdb=" O GLN D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 306 through 324 removed outlier: 3.734A pdb=" N ARG D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.814A pdb=" N LYS D 343 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 356 removed outlier: 3.669A pdb=" N LYS D 356 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 394 Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 427 through 443 removed outlier: 3.765A pdb=" N GLN D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 441 " --> pdb=" O GLY D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 462 Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.673A pdb=" N THR C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 64 removed outlier: 6.405A pdb=" N TRP C 40 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 54 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET C 38 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 97 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 116 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 73 through 81 removed outlier: 13.085A pdb=" N ASN D 416 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N CYS D 275 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N GLU D 418 " --> pdb=" O CYS D 275 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU D 277 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE D 420 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG D 279 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN D 422 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE D 281 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N LYS D 424 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE D 269 " --> pdb=" O ILE D 405 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 407 " --> pdb=" O PHE D 269 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET D 221 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 73 through 81 removed outlier: 13.085A pdb=" N ASN D 416 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N CYS D 275 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N GLU D 418 " --> pdb=" O CYS D 275 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU D 277 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE D 420 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG D 279 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN D 422 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE D 281 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N LYS D 424 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 189 removed outlier: 6.941A pdb=" N LYS D 193 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN D 94 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 173 through 174 195 hydrogen bonds defined for protein. 531 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: 0.57 Time building geometry restraints manager: 0.38 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: 1313 1.34 - 1.46: 1034 1.46 - 1.59: 1704 1.59 - 1.71: 0 1.71 - 1.83: 42 Bond restraints: 4093 Sorted by residual: bond pdb=" CG ASN D 368 " pdb=" ND2 ASN D 368 " ideal model delta sigma weight residual 1.328 1.394 -0.066 2.10e-02 2.27e+03 9.93e+00 bond pdb=" N CYS D 179 " pdb=" CA CYS D 179 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.22e-02 6.72e+03 8.11e+00 bond pdb=" N ASP D 296 " pdb=" CA ASP D 296 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.16e-02 7.43e+03 7.83e+00 bond pdb=" N LEU D 299 " pdb=" CA LEU D 299 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.23e-02 6.61e+03 7.03e+00 bond pdb=" N SER D 297 " pdb=" CA SER D 297 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.18e-02 7.18e+03 6.37e+00 ... (remaining 4088 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 5323 1.72 - 3.45: 207 3.45 - 5.17: 33 5.17 - 6.90: 5 6.90 - 8.62: 3 Bond angle restraints: 5571 Sorted by residual: angle pdb=" C CYS D 345 " pdb=" N ALA D 346 " pdb=" CA ALA D 346 " ideal model delta sigma weight residual 122.56 114.80 7.76 1.50e+00 4.44e-01 2.68e+01 angle pdb=" N SER C 106 " pdb=" CA SER C 106 " pdb=" C SER C 106 " ideal model delta sigma weight residual 112.54 117.59 -5.05 1.22e+00 6.72e-01 1.71e+01 angle pdb=" C CYS D 345 " pdb=" CA CYS D 345 " pdb=" CB CYS D 345 " ideal model delta sigma weight residual 110.42 102.58 7.84 1.99e+00 2.53e-01 1.55e+01 angle pdb=" N ASP D 298 " pdb=" CA ASP D 298 " pdb=" C ASP D 298 " ideal model delta sigma weight residual 112.72 107.98 4.74 1.36e+00 5.41e-01 1.21e+01 angle pdb=" N SER C 107 " pdb=" CA SER C 107 " pdb=" C SER C 107 " ideal model delta sigma weight residual 109.39 114.88 -5.49 1.59e+00 3.96e-01 1.19e+01 ... (remaining 5566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 2175 16.61 - 33.23: 181 33.23 - 49.84: 40 49.84 - 66.46: 8 66.46 - 83.07: 5 Dihedral angle restraints: 2409 sinusoidal: 837 harmonic: 1572 Sorted by residual: dihedral pdb=" CB CYS D 323 " pdb=" SG CYS D 323 " pdb=" SG CYS D 345 " pdb=" CB CYS D 345 " ideal model delta sinusoidal sigma weight residual 93.00 169.27 -76.27 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS D 93 " pdb=" SG CYS D 93 " pdb=" SG CYS D 194 " pdb=" CB CYS D 194 " ideal model delta sinusoidal sigma weight residual 93.00 37.25 55.75 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CA CYS D 323 " pdb=" C CYS D 323 " pdb=" N ASN D 324 " pdb=" CA ASN D 324 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 2406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.627: 619 0.627 - 1.255: 1 1.255 - 1.882: 0 1.882 - 2.510: 0 2.510 - 3.137: 1 Chirality restraints: 621 Sorted by residual: chirality pdb=" C1 NAG D 602 " pdb=" ND2 ASN D 395 " pdb=" C2 NAG D 602 " pdb=" O5 NAG D 602 " both_signs ideal model delta sigma weight residual False -2.40 0.74 -3.14 2.00e-01 2.50e+01 2.46e+02 chirality pdb=" C1 NAG D 601 " pdb=" ND2 ASN D 368 " pdb=" C2 NAG D 601 " pdb=" O5 NAG D 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-01 2.50e+01 3.42e+01 chirality pdb=" CA TYR C 108 " pdb=" N TYR C 108 " pdb=" C TYR C 108 " pdb=" CB TYR C 108 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 618 not shown) Planarity restraints: 732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 395 " 0.073 2.00e-02 2.50e+03 2.02e-01 5.11e+02 pdb=" CG ASN D 395 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN D 395 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN D 395 " -0.329 2.00e-02 2.50e+03 pdb=" C1 NAG D 602 " 0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 368 " 0.141 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" CG ASN D 368 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN D 368 " -0.128 2.00e-02 2.50e+03 pdb=" ND2 ASN D 368 " -0.169 2.00e-02 2.50e+03 pdb=" C1 NAG D 601 " 0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 395 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" CG ASN D 395 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN D 395 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 395 " -0.015 2.00e-02 2.50e+03 ... (remaining 729 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 20 2.52 - 3.12: 2985 3.12 - 3.71: 5730 3.71 - 4.31: 8216 4.31 - 4.90: 14059 Nonbonded interactions: 31010 Sorted by model distance: nonbonded pdb=" ND2 ASN D 395 " pdb=" N2 NAG D 602 " model vdw 1.929 2.560 nonbonded pdb=" OD1 ASN D 368 " pdb=" C1 NAG D 601 " model vdw 2.033 2.776 nonbonded pdb=" NE ARG C 35 " pdb=" OD2 ASP D 298 " model vdw 2.171 3.120 nonbonded pdb=" OH TYR D 305 " pdb=" O GLU D 364 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR C 32 " pdb=" OD2 ASP D 298 " model vdw 2.270 3.040 ... (remaining 31005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.340 Find NCS groups from input model: 0.020 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 : 0.013 0.658 4102 Z= 0.646 Angle : 1.621 64.650 5591 Z= 0.657 Chirality : 0.143 3.137 621 Planarity : 0.004 0.050 730 Dihedral : 13.562 83.073 1382 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.55 % Allowed : 0.00 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.11 (0.37), residues: 536 helix: -0.34 (0.44), residues: 136 sheet: -0.74 (0.43), residues: 140 loop : -0.82 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 105 TYR 0.034 0.002 TYR D 426 PHE 0.023 0.002 PHE D 257 TRP 0.008 0.002 TRP C 40 HIS 0.002 0.001 HIS D 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.36 ( 4093) covalent geometry : angle 0.80440 / 0.46 ( 5571) SS BOND : bond 0.00965 / 0.47 ( 7) SS BOND : angle 3.00584 / 1.59 ( 14) hydrogen bonds : bond 0.17814 / 13.70 ( 187) hydrogen bonds : angle 7.80325 / 5.59 ( 531) link_NAG-ASN : bond 0.48800 / 23.47 ( 2) link_NAG-ASN : angle 42.72786 / 23.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 129 MET cc_start: 0.1470 (mmm) cc_final: 0.0955 (ptm) outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 0.4739 time to fit residues: 32.4967 Evaluate side-chains 40 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 110 HIS D 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.095059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067658 restraints weight = 8534.080| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.16 r_work: 0.2878 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4102 Z= 0.121 Angle : 0.653 12.139 5591 Z= 0.323 Chirality : 0.043 0.212 621 Planarity : 0.004 0.045 730 Dihedral : 5.115 57.434 589 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.37 % Allowed : 9.29 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.38), residues: 536 helix: 0.49 (0.44), residues: 144 sheet: -0.58 (0.44), residues: 139 loop : -0.22 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 204 TYR 0.021 0.001 TYR D 360 PHE 0.012 0.001 PHE D 100 TRP 0.007 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 4093) covalent geometry : angle 0.63111 / 0.32 ( 5571) SS BOND : bond 0.00213 / 0.16 ( 7) SS BOND : angle 2.11245 / 1.25 ( 14) hydrogen bonds : bond 0.03571 / 2.75 ( 187) hydrogen bonds : angle 5.53170 / 3.98 ( 531) link_NAG-ASN : bond 0.00856 / 0.42 ( 2) link_NAG-ASN : angle 4.15537 / 2.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: C 38 MET cc_start: 0.8845 (mmm) cc_final: 0.8564 (mmm) REVERT: C 64 TYR cc_start: 0.8584 (m-80) cc_final: 0.8014 (m-80) REVERT: C 72 PHE cc_start: 0.8506 (m-80) cc_final: 0.8243 (m-80) REVERT: C 77 ASP cc_start: 0.8066 (t0) cc_final: 0.7735 (t0) REVERT: C 84 TYR cc_start: 0.8346 (m-10) cc_final: 0.8087 (m-80) REVERT: C 85 LEU cc_start: 0.8099 (tt) cc_final: 0.7687 (tt) REVERT: D 129 MET cc_start: -0.0029 (mmm) cc_final: -0.0764 (ptm) REVERT: D 365 MET cc_start: 0.8695 (ttp) cc_final: 0.8340 (ttm) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.4263 time to fit residues: 24.1325 Evaluate side-chains 45 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.095143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.068103 restraints weight = 8345.621| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.13 r_work: 0.2879 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4102 Z= 0.120 Angle : 0.565 10.525 5591 Z= 0.280 Chirality : 0.043 0.234 621 Planarity : 0.004 0.041 730 Dihedral : 4.865 57.492 589 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.19 % Allowed : 12.30 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.02 (0.39), residues: 536 helix: 0.66 (0.44), residues: 150 sheet: -0.33 (0.46), residues: 139 loop : -0.02 (0.45), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 201 TYR 0.014 0.001 TYR D 360 PHE 0.006 0.001 PHE D 263 TRP 0.005 0.001 TRP D 233 HIS 0.005 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4093) covalent geometry : angle 0.55762 / 0.28 ( 5571) SS BOND : bond 0.00240 / 0.15 ( 7) SS BOND : angle 1.44672 / 0.86 ( 14) hydrogen bonds : bond 0.03078 / 2.33 ( 187) hydrogen bonds : angle 4.96211 / 3.55 ( 531) link_NAG-ASN : bond 0.00147 / 0.07 ( 2) link_NAG-ASN : angle 1.99758 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.163 Fit side-chains REVERT: C 38 MET cc_start: 0.8943 (mmm) cc_final: 0.8594 (mmm) REVERT: C 64 TYR cc_start: 0.8613 (m-80) cc_final: 0.7925 (m-80) REVERT: C 77 ASP cc_start: 0.8157 (t0) cc_final: 0.7933 (t0) REVERT: C 81 ASN cc_start: 0.8687 (m-40) cc_final: 0.8452 (m-40) REVERT: C 85 LEU cc_start: 0.7916 (tt) cc_final: 0.7561 (tt) REVERT: D 98 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8630 (p90) REVERT: D 129 MET cc_start: 0.0665 (mmm) cc_final: -0.0432 (ptm) REVERT: D 134 GLN cc_start: 0.8142 (mm110) cc_final: 0.7923 (mm-40) REVERT: D 242 GLU cc_start: 0.8737 (pm20) cc_final: 0.8293 (pm20) REVERT: D 365 MET cc_start: 0.8560 (ttp) cc_final: 0.8172 (ttm) outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 0.4689 time to fit residues: 22.5790 Evaluate side-chains 45 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.066144 restraints weight = 8348.697| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.13 r_work: 0.2844 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4102 Z= 0.146 Angle : 0.551 9.286 5591 Z= 0.276 Chirality : 0.044 0.303 621 Planarity : 0.004 0.039 730 Dihedral : 4.209 16.836 588 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.91 % Allowed : 14.75 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.15 (0.39), residues: 536 helix: 0.79 (0.45), residues: 151 sheet: -0.32 (0.45), residues: 139 loop : 0.09 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 201 TYR 0.011 0.001 TYR D 360 PHE 0.006 0.001 PHE D 263 TRP 0.006 0.001 TRP C 40 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 4093) covalent geometry : angle 0.54456 / 0.27 ( 5571) SS BOND : bond 0.00162 / 0.13 ( 7) SS BOND : angle 1.48531 / 0.89 ( 14) hydrogen bonds : bond 0.03060 / 2.30 ( 187) hydrogen bonds : angle 4.81257 / 3.44 ( 531) link_NAG-ASN : bond 0.00320 / 0.16 ( 2) link_NAG-ASN : angle 1.42927 / 0.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9033 (m) cc_final: 0.8667 (p) REVERT: C 64 TYR cc_start: 0.8570 (m-80) cc_final: 0.7872 (m-80) REVERT: C 81 ASN cc_start: 0.8620 (m-40) cc_final: 0.8370 (m-40) REVERT: C 84 TYR cc_start: 0.8273 (m-10) cc_final: 0.7932 (m-80) REVERT: C 85 LEU cc_start: 0.7945 (tt) cc_final: 0.7574 (tt) REVERT: D 98 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8729 (p90) REVERT: D 154 MET cc_start: 0.9010 (mmt) cc_final: 0.8772 (tpp) REVERT: D 242 GLU cc_start: 0.8755 (pm20) cc_final: 0.8290 (pm20) REVERT: D 365 MET cc_start: 0.8460 (ttp) cc_final: 0.8066 (ttm) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.4751 time to fit residues: 23.7741 Evaluate side-chains 45 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.092213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.065234 restraints weight = 8506.960| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.10 r_work: 0.2820 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4102 Z= 0.217 Angle : 0.594 7.429 5591 Z= 0.299 Chirality : 0.045 0.292 621 Planarity : 0.004 0.037 730 Dihedral : 4.431 18.649 588 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.46 % Allowed : 15.57 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.38), residues: 536 helix: 1.15 (0.46), residues: 143 sheet: -0.43 (0.43), residues: 146 loop : 0.09 (0.44), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 201 TYR 0.012 0.002 TYR C 108 PHE 0.008 0.001 PHE D 241 TRP 0.006 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 ( 4093) covalent geometry : angle 0.58523 / 0.30 ( 5571) SS BOND : bond 0.00250 / 0.21 ( 7) SS BOND : angle 1.63152 / 0.97 ( 14) hydrogen bonds : bond 0.03329 / 2.51 ( 187) hydrogen bonds : angle 4.86036 / 3.47 ( 531) link_NAG-ASN : bond 0.00183 / 0.09 ( 2) link_NAG-ASN : angle 2.00354 / 1.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.171 Fit side-chains REVERT: C 34 SER cc_start: 0.9114 (m) cc_final: 0.8550 (p) REVERT: C 57 SER cc_start: 0.9173 (p) cc_final: 0.8551 (t) REVERT: C 64 TYR cc_start: 0.8331 (m-80) cc_final: 0.7688 (m-80) REVERT: C 84 TYR cc_start: 0.8301 (m-10) cc_final: 0.7954 (m-80) REVERT: C 85 LEU cc_start: 0.7873 (tt) cc_final: 0.7449 (tt) REVERT: D 98 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8728 (p90) REVERT: D 242 GLU cc_start: 0.8819 (pm20) cc_final: 0.8338 (pm20) REVERT: D 365 MET cc_start: 0.8467 (ttp) cc_final: 0.8023 (ttm) outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.4146 time to fit residues: 20.0684 Evaluate side-chains 44 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 40.0000 chunk 41 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066922 restraints weight = 8561.525| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.07 r_work: 0.2833 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4102 Z= 0.153 Angle : 0.548 7.152 5591 Z= 0.278 Chirality : 0.044 0.268 621 Planarity : 0.004 0.044 730 Dihedral : 4.238 19.355 588 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.46 % Allowed : 16.39 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.19 (0.39), residues: 536 helix: 0.96 (0.45), residues: 151 sheet: -0.34 (0.45), residues: 139 loop : 0.06 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 201 TYR 0.008 0.001 TYR D 360 PHE 0.014 0.001 PHE C 72 TRP 0.007 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4093) covalent geometry : angle 0.53908 / 0.28 ( 5571) SS BOND : bond 0.00270 / 0.22 ( 7) SS BOND : angle 1.71716 / 1.02 ( 14) hydrogen bonds : bond 0.03165 / 2.38 ( 187) hydrogen bonds : angle 4.79584 / 3.43 ( 531) link_NAG-ASN : bond 0.00233 / 0.11 ( 2) link_NAG-ASN : angle 1.73788 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9116 (m) cc_final: 0.8557 (p) REVERT: C 38 MET cc_start: 0.8365 (mmt) cc_final: 0.7703 (mmm) REVERT: C 57 SER cc_start: 0.9146 (p) cc_final: 0.8462 (t) REVERT: C 64 TYR cc_start: 0.8334 (m-80) cc_final: 0.7654 (m-80) REVERT: C 84 TYR cc_start: 0.8286 (m-10) cc_final: 0.7982 (m-80) REVERT: C 85 LEU cc_start: 0.7912 (tt) cc_final: 0.7398 (tt) REVERT: D 98 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8762 (p90) REVERT: D 242 GLU cc_start: 0.8796 (pm20) cc_final: 0.8317 (pm20) REVERT: D 365 MET cc_start: 0.8457 (ttp) cc_final: 0.8007 (ttm) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 0.4425 time to fit residues: 22.7406 Evaluate side-chains 43 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.094274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067307 restraints weight = 8571.597| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.13 r_work: 0.2859 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4102 Z= 0.102 Angle : 0.505 6.737 5591 Z= 0.257 Chirality : 0.043 0.260 621 Planarity : 0.003 0.042 730 Dihedral : 3.909 16.469 588 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.91 % Allowed : 18.03 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.34 (0.39), residues: 536 helix: 1.20 (0.45), residues: 151 sheet: -0.31 (0.45), residues: 139 loop : 0.10 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 201 TYR 0.006 0.001 TYR D 417 PHE 0.006 0.001 PHE D 272 TRP 0.006 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 4093) covalent geometry : angle 0.49816 / 0.25 ( 5571) SS BOND : bond 0.00156 / 0.12 ( 7) SS BOND : angle 1.33469 / 0.79 ( 14) hydrogen bonds : bond 0.02934 / 2.17 ( 187) hydrogen bonds : angle 4.64262 / 3.32 ( 531) link_NAG-ASN : bond 0.00363 / 0.18 ( 2) link_NAG-ASN : angle 1.63406 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9112 (m) cc_final: 0.8529 (p) REVERT: C 38 MET cc_start: 0.8378 (mmt) cc_final: 0.7255 (mmm) REVERT: C 57 SER cc_start: 0.9142 (p) cc_final: 0.8418 (t) REVERT: C 64 TYR cc_start: 0.8378 (m-80) cc_final: 0.7731 (m-80) REVERT: C 72 PHE cc_start: 0.8309 (m-80) cc_final: 0.8001 (m-80) REVERT: C 84 TYR cc_start: 0.8210 (m-10) cc_final: 0.7944 (m-80) REVERT: C 85 LEU cc_start: 0.7861 (tt) cc_final: 0.7368 (tt) REVERT: D 84 GLN cc_start: 0.8646 (mt0) cc_final: 0.8354 (mt0) REVERT: D 242 GLU cc_start: 0.8729 (pm20) cc_final: 0.8232 (pm20) REVERT: D 418 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7885 (mt-10) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.4536 time to fit residues: 22.7887 Evaluate side-chains 49 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 35 optimal weight: 0.0030 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.065902 restraints weight = 8404.959| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.11 r_work: 0.2836 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4102 Z= 0.159 Angle : 0.532 6.781 5591 Z= 0.271 Chirality : 0.043 0.251 621 Planarity : 0.003 0.042 730 Dihedral : 4.105 19.147 588 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.64 % Allowed : 18.03 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.42 (0.39), residues: 536 helix: 1.26 (0.46), residues: 149 sheet: -0.24 (0.45), residues: 137 loop : 0.13 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 201 TYR 0.011 0.001 TYR C 99 PHE 0.005 0.001 PHE D 69 TRP 0.006 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 4093) covalent geometry : angle 0.52480 / 0.27 ( 5571) SS BOND : bond 0.00162 / 0.13 ( 7) SS BOND : angle 1.46663 / 0.86 ( 14) hydrogen bonds : bond 0.03103 / 2.33 ( 187) hydrogen bonds : angle 4.70446 / 3.36 ( 531) link_NAG-ASN : bond 0.00206 / 0.10 ( 2) link_NAG-ASN : angle 1.81245 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9139 (m) cc_final: 0.8555 (p) REVERT: C 38 MET cc_start: 0.8391 (mmt) cc_final: 0.7713 (mmm) REVERT: C 57 SER cc_start: 0.9087 (p) cc_final: 0.8391 (t) REVERT: C 64 TYR cc_start: 0.8362 (m-80) cc_final: 0.7681 (m-80) REVERT: C 85 LEU cc_start: 0.7876 (tt) cc_final: 0.7419 (tt) REVERT: D 242 GLU cc_start: 0.8756 (pm20) cc_final: 0.8248 (pm20) REVERT: D 418 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7958 (mt-10) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.4520 time to fit residues: 22.2653 Evaluate side-chains 44 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.065348 restraints weight = 8610.529| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.12 r_work: 0.2823 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4102 Z= 0.192 Angle : 0.560 6.649 5591 Z= 0.285 Chirality : 0.044 0.253 621 Planarity : 0.004 0.050 730 Dihedral : 4.279 22.788 588 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.64 % Allowed : 19.13 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.35 (0.39), residues: 536 helix: 1.21 (0.46), residues: 149 sheet: -0.34 (0.44), residues: 139 loop : 0.13 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 201 TYR 0.012 0.001 TYR C 99 PHE 0.007 0.001 PHE D 241 TRP 0.006 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 4093) covalent geometry : angle 0.55129 / 0.28 ( 5571) SS BOND : bond 0.00196 / 0.16 ( 7) SS BOND : angle 1.56978 / 0.92 ( 14) hydrogen bonds : bond 0.03249 / 2.46 ( 187) hydrogen bonds : angle 4.76187 / 3.41 ( 531) link_NAG-ASN : bond 0.00146 / 0.07 ( 2) link_NAG-ASN : angle 1.94913 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9131 (m) cc_final: 0.8565 (p) REVERT: C 57 SER cc_start: 0.9107 (p) cc_final: 0.8368 (t) REVERT: C 64 TYR cc_start: 0.8294 (m-80) cc_final: 0.7625 (m-80) REVERT: C 84 TYR cc_start: 0.8253 (m-10) cc_final: 0.7939 (m-80) REVERT: C 85 LEU cc_start: 0.7915 (tt) cc_final: 0.7499 (tt) REVERT: D 242 GLU cc_start: 0.8799 (pm20) cc_final: 0.8281 (pm20) REVERT: D 418 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7983 (mt-10) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.4623 time to fit residues: 21.3334 Evaluate side-chains 42 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.094407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067673 restraints weight = 8439.307| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.07 r_work: 0.2861 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4102 Z= 0.106 Angle : 0.511 6.466 5591 Z= 0.260 Chirality : 0.043 0.266 621 Planarity : 0.004 0.043 730 Dihedral : 3.960 19.373 588 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.09 % Allowed : 19.67 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.41 (0.39), residues: 536 helix: 1.35 (0.46), residues: 149 sheet: -0.29 (0.46), residues: 132 loop : 0.07 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 201 TYR 0.012 0.001 TYR C 99 PHE 0.006 0.001 PHE D 272 TRP 0.008 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 4093) covalent geometry : angle 0.50637 / 0.26 ( 5571) SS BOND : bond 0.00148 / 0.11 ( 7) SS BOND : angle 1.20829 / 0.71 ( 14) hydrogen bonds : bond 0.02952 / 2.19 ( 187) hydrogen bonds : angle 4.61208 / 3.29 ( 531) link_NAG-ASN : bond 0.00299 / 0.14 ( 2) link_NAG-ASN : angle 1.37541 / 0.73 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.163 Fit side-chains REVERT: C 34 SER cc_start: 0.9190 (m) cc_final: 0.8662 (p) REVERT: C 57 SER cc_start: 0.9113 (p) cc_final: 0.8283 (t) REVERT: C 64 TYR cc_start: 0.8337 (m-80) cc_final: 0.7640 (m-80) REVERT: C 84 TYR cc_start: 0.8237 (m-10) cc_final: 0.7913 (m-80) REVERT: C 85 LEU cc_start: 0.7847 (tt) cc_final: 0.7426 (tt) REVERT: D 242 GLU cc_start: 0.8694 (pm20) cc_final: 0.8189 (pm20) REVERT: D 418 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8061 (mt-10) outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.4143 time to fit residues: 18.7195 Evaluate side-chains 43 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 8.9990 chunk 28 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.094693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.067976 restraints weight = 8504.717| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.09 r_work: 0.2873 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4102 Z= 0.106 Angle : 0.498 6.460 5591 Z= 0.252 Chirality : 0.043 0.263 621 Planarity : 0.004 0.043 730 Dihedral : 3.801 16.154 588 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.09 % Allowed : 19.40 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.56 (0.39), residues: 536 helix: 1.54 (0.46), residues: 149 sheet: -0.19 (0.46), residues: 130 loop : 0.11 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 201 TYR 0.008 0.001 TYR D 360 PHE 0.005 0.001 PHE D 50 TRP 0.007 0.001 TRP C 40 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 4093) covalent geometry : angle 0.49341 / 0.25 ( 5571) SS BOND : bond 0.00149 / 0.11 ( 7) SS BOND : angle 1.17977 / 0.69 ( 14) hydrogen bonds : bond 0.02874 / 2.16 ( 187) hydrogen bonds : angle 4.53764 / 3.24 ( 531) link_NAG-ASN : bond 0.00261 / 0.13 ( 2) link_NAG-ASN : angle 1.24491 / 0.66 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1449.45 seconds wall clock time: 25 minutes 27.46 seconds (1527.46 seconds total)