Starting phenix.real_space_refine on Tue Feb 11 04:14:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rnn_24580/02_2025/7rnn_24580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rnn_24580/02_2025/7rnn_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_24580/02_2025/7rnn_24580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rnn_24580/02_2025/7rnn_24580.map" model { file = "/net/cci-nas-00/data/ceres_data/7rnn_24580/02_2025/7rnn_24580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rnn_24580/02_2025/7rnn_24580.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 3} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.45, per 1000 atoms: 0.86 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: 0.95 Conformation dependent library (CDL) restraints added in 499.3 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: 0.53 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: 1.27 Time building geometry restraints manager: 1.12 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 - 24.58: 2324 24.58 - 49.16: 104 49.16 - 73.74: 15 73.74 - 98.32: 5 98.32 - 122.91: 3 Dihedral angle restraints: 2451 sinusoidal: 879 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 2448 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: 1.760 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.330 Find NCS groups from input model: 0.040 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:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 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 : 0.008 0.066 4093 Z= 0.516 Angle : 0.804 8.621 5571 Z= 0.458 Chirality : 0.143 3.137 621 Planarity : 0.004 0.050 730 Dihedral : 14.961 122.906 1424 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (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 TRP 0.008 0.002 TRP C 40 HIS 0.002 0.001 HIS D 163 PHE 0.023 0.002 PHE D 257 TYR 0.034 0.002 TYR D 426 ARG 0.010 0.001 ARG C 105 *********************** 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 : 0.489 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: 1.0910 time to fit residues: 74.9794 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 : 0.492 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 21 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.095272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.068139 restraints weight = 8437.529| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.12 r_work: 0.2881 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4093 Z= 0.163 Angle : 0.631 11.407 5571 Z= 0.315 Chirality : 0.041 0.145 621 Planarity : 0.004 0.044 730 Dihedral : 7.588 58.076 631 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.37 % Allowed : 9.56 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.38), residues: 536 helix: 0.50 (0.44), residues: 144 sheet: -0.55 (0.44), residues: 139 loop : -0.20 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.012 0.001 PHE D 352 TYR 0.017 0.001 TYR D 360 ARG 0.007 0.001 ARG D 204 *********************** 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 55 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.451 Fit side-chains REVERT: C 38 MET cc_start: 0.8852 (mmm) cc_final: 0.8473 (mmm) REVERT: C 64 TYR cc_start: 0.8576 (m-80) cc_final: 0.7997 (m-80) REVERT: C 72 PHE cc_start: 0.8468 (m-80) cc_final: 0.8226 (m-80) REVERT: C 77 ASP cc_start: 0.8063 (t0) cc_final: 0.7724 (t0) REVERT: C 84 TYR cc_start: 0.8325 (m-10) cc_final: 0.8067 (m-80) REVERT: C 85 LEU cc_start: 0.8045 (tt) cc_final: 0.7626 (tt) REVERT: D 129 MET cc_start: 0.0308 (mmm) cc_final: -0.0602 (ptm) REVERT: D 365 MET cc_start: 0.8638 (ttp) cc_final: 0.8294 (ttm) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.9555 time to fit residues: 53.1309 Evaluate side-chains 43 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL 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 12 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 45 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.095572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.068126 restraints weight = 8374.711| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.18 r_work: 0.2879 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4093 Z= 0.157 Angle : 0.530 7.254 5571 Z= 0.271 Chirality : 0.040 0.148 621 Planarity : 0.004 0.041 730 Dihedral : 5.246 33.109 630 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.39), residues: 536 helix: 0.88 (0.45), residues: 145 sheet: -0.38 (0.44), residues: 147 loop : 0.01 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.005 0.001 PHE D 263 TYR 0.013 0.001 TYR D 360 ARG 0.007 0.001 ARG D 201 *********************** 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 52 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: C 38 MET cc_start: 0.8916 (mmm) cc_final: 0.8573 (mmm) REVERT: C 64 TYR cc_start: 0.8590 (m-80) cc_final: 0.7826 (m-80) REVERT: C 72 PHE cc_start: 0.8444 (m-80) cc_final: 0.8100 (m-80) REVERT: C 77 ASP cc_start: 0.8169 (t0) cc_final: 0.7945 (t0) REVERT: C 81 ASN cc_start: 0.8643 (m-40) cc_final: 0.8432 (m-40) REVERT: C 85 LEU cc_start: 0.7960 (tt) cc_final: 0.7585 (tt) REVERT: D 98 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8533 (p90) REVERT: D 129 MET cc_start: 0.0605 (mmm) cc_final: -0.0451 (ptm) REVERT: D 134 GLN cc_start: 0.8109 (mm110) cc_final: 0.7899 (mm-40) REVERT: D 242 GLU cc_start: 0.8727 (pm20) cc_final: 0.8287 (pm20) REVERT: D 365 MET cc_start: 0.8592 (ttp) cc_final: 0.8206 (ttm) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 1.0318 time to fit residues: 51.8558 Evaluate side-chains 47 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.091746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.064809 restraints weight = 8530.074| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.12 r_work: 0.2799 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4093 Z= 0.405 Angle : 0.620 7.669 5571 Z= 0.319 Chirality : 0.043 0.151 621 Planarity : 0.004 0.038 730 Dihedral : 5.554 37.467 630 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.19 % Allowed : 14.75 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.38), residues: 536 helix: 0.96 (0.46), residues: 143 sheet: -0.50 (0.42), residues: 146 loop : 0.02 (0.44), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.010 0.002 PHE D 241 TYR 0.015 0.002 TYR C 104 ARG 0.008 0.001 ARG D 201 *********************** 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 48 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9092 (m) cc_final: 0.8767 (p) REVERT: C 64 TYR cc_start: 0.8395 (m-80) cc_final: 0.7803 (m-80) REVERT: C 81 ASN cc_start: 0.8593 (m-40) cc_final: 0.8388 (m-40) REVERT: C 84 TYR cc_start: 0.8238 (m-10) cc_final: 0.7903 (m-80) REVERT: C 85 LEU cc_start: 0.7781 (tt) cc_final: 0.7370 (tt) REVERT: D 98 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8674 (p90) REVERT: D 242 GLU cc_start: 0.8840 (pm20) cc_final: 0.8363 (pm20) REVERT: D 365 MET cc_start: 0.8505 (ttp) cc_final: 0.8081 (ttm) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 1.0368 time to fit residues: 49.8396 Evaluate side-chains 44 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 447 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.065453 restraints weight = 8609.886| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.13 r_work: 0.2822 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4093 Z= 0.267 Angle : 0.550 7.043 5571 Z= 0.286 Chirality : 0.041 0.141 621 Planarity : 0.004 0.043 730 Dihedral : 5.226 36.405 630 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.91 % Allowed : 16.67 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.38), residues: 536 helix: 1.03 (0.45), residues: 145 sheet: -0.49 (0.43), residues: 146 loop : 0.05 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.025 0.002 PHE D 92 TYR 0.009 0.001 TYR C 104 ARG 0.009 0.001 ARG D 201 *********************** 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 47 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9080 (m) cc_final: 0.8556 (p) REVERT: C 57 SER cc_start: 0.9173 (p) cc_final: 0.8529 (t) REVERT: C 64 TYR cc_start: 0.8329 (m-80) cc_final: 0.7729 (m-80) REVERT: C 85 LEU cc_start: 0.7880 (tt) cc_final: 0.7382 (tt) REVERT: D 98 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8728 (p90) REVERT: D 242 GLU cc_start: 0.8808 (pm20) cc_final: 0.8314 (pm20) REVERT: D 365 MET cc_start: 0.8451 (ttp) cc_final: 0.8018 (ttm) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.9266 time to fit residues: 44.7924 Evaluate side-chains 42 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 51 optimal weight: 5.9990 chunk 30 optimal weight: 0.0050 chunk 2 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.093147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.066193 restraints weight = 8485.789| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.12 r_work: 0.2839 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4093 Z= 0.184 Angle : 0.508 6.589 5571 Z= 0.265 Chirality : 0.040 0.139 621 Planarity : 0.004 0.042 730 Dihedral : 4.950 36.641 630 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.46 % Allowed : 16.94 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.38), residues: 536 helix: 1.01 (0.45), residues: 151 sheet: -0.43 (0.44), residues: 139 loop : 0.09 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 40 HIS 0.004 0.001 HIS D 250 PHE 0.021 0.001 PHE D 92 TYR 0.011 0.001 TYR C 99 ARG 0.010 0.001 ARG D 201 *********************** 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 51 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9099 (m) cc_final: 0.8569 (p) REVERT: C 57 SER cc_start: 0.9160 (p) cc_final: 0.8477 (t) REVERT: C 64 TYR cc_start: 0.8364 (m-80) cc_final: 0.7659 (m-80) REVERT: C 84 TYR cc_start: 0.8241 (m-10) cc_final: 0.7917 (m-80) REVERT: C 85 LEU cc_start: 0.7895 (tt) cc_final: 0.7390 (tt) REVERT: D 84 GLN cc_start: 0.8652 (mt0) cc_final: 0.8413 (mt0) REVERT: D 98 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8761 (p90) REVERT: D 242 GLU cc_start: 0.8778 (pm20) cc_final: 0.8306 (pm20) REVERT: D 365 MET cc_start: 0.8474 (ttp) cc_final: 0.8032 (ttm) REVERT: D 418 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8138 (mt-10) outliers start: 9 outliers final: 5 residues processed: 49 average time/residue: 0.9395 time to fit residues: 48.5188 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 : 0.420 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.0370 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.065369 restraints weight = 8465.677| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.16 r_work: 0.2822 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4093 Z= 0.273 Angle : 0.538 6.757 5571 Z= 0.278 Chirality : 0.041 0.143 621 Planarity : 0.004 0.037 730 Dihedral : 5.126 37.929 630 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.19 % Allowed : 17.21 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.38), residues: 536 helix: 1.12 (0.45), residues: 149 sheet: -0.47 (0.44), residues: 139 loop : 0.09 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 PHE 0.017 0.001 PHE D 92 TYR 0.009 0.001 TYR D 389 ARG 0.008 0.001 ARG D 201 *********************** 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 49 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9125 (m) cc_final: 0.8574 (p) REVERT: C 57 SER cc_start: 0.9127 (p) cc_final: 0.8429 (t) REVERT: C 64 TYR cc_start: 0.8314 (m-80) cc_final: 0.7576 (m-80) REVERT: C 84 TYR cc_start: 0.8260 (m-10) cc_final: 0.7907 (m-80) REVERT: C 85 LEU cc_start: 0.7862 (tt) cc_final: 0.7415 (tt) REVERT: D 98 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8788 (p90) REVERT: D 242 GLU cc_start: 0.8834 (pm20) cc_final: 0.8359 (pm20) REVERT: D 365 MET cc_start: 0.8455 (ttp) cc_final: 0.8004 (ttm) REVERT: D 418 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7999 (mt-10) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.9632 time to fit residues: 48.6021 Evaluate side-chains 46 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 447 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.065695 restraints weight = 8273.762| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.08 r_work: 0.2831 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4093 Z= 0.263 Angle : 0.532 6.677 5571 Z= 0.276 Chirality : 0.041 0.142 621 Planarity : 0.004 0.047 730 Dihedral : 5.133 37.883 630 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.01 % Allowed : 17.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.38), residues: 536 helix: 1.15 (0.45), residues: 149 sheet: -0.52 (0.43), residues: 139 loop : 0.11 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 PHE 0.017 0.001 PHE D 92 TYR 0.008 0.001 TYR D 389 ARG 0.009 0.001 ARG D 201 *********************** 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 51 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9146 (m) cc_final: 0.8576 (p) REVERT: C 57 SER cc_start: 0.9127 (p) cc_final: 0.8369 (t) REVERT: C 64 TYR cc_start: 0.8313 (m-80) cc_final: 0.7584 (m-80) REVERT: C 84 TYR cc_start: 0.8279 (m-10) cc_final: 0.7913 (m-80) REVERT: C 85 LEU cc_start: 0.7856 (tt) cc_final: 0.7424 (tt) REVERT: D 98 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8725 (p90) REVERT: D 242 GLU cc_start: 0.8773 (pm20) cc_final: 0.8266 (pm20) REVERT: D 365 MET cc_start: 0.8446 (ttp) cc_final: 0.7999 (ttm) REVERT: D 418 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7982 (mt-10) outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 0.9003 time to fit residues: 46.4293 Evaluate side-chains 44 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.093956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067210 restraints weight = 8431.847| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.10 r_work: 0.2851 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4093 Z= 0.170 Angle : 0.498 6.307 5571 Z= 0.259 Chirality : 0.040 0.136 621 Planarity : 0.003 0.043 730 Dihedral : 4.834 37.113 630 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.64 % Allowed : 18.58 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.38), residues: 536 helix: 1.27 (0.46), residues: 149 sheet: -0.44 (0.45), residues: 132 loop : 0.10 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.017 0.001 PHE D 92 TYR 0.006 0.001 TYR D 417 ARG 0.009 0.001 ARG D 201 *********************** 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 : 0.509 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9140 (m) cc_final: 0.8554 (p) REVERT: C 57 SER cc_start: 0.9128 (p) cc_final: 0.8329 (t) REVERT: C 64 TYR cc_start: 0.8350 (m-80) cc_final: 0.7618 (m-80) REVERT: C 84 TYR cc_start: 0.8301 (m-10) cc_final: 0.7959 (m-80) REVERT: C 85 LEU cc_start: 0.7762 (tt) cc_final: 0.7303 (tt) REVERT: D 98 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8810 (p90) REVERT: D 242 GLU cc_start: 0.8719 (pm20) cc_final: 0.8207 (pm20) REVERT: D 418 GLU cc_start: 0.8564 (mt-10) cc_final: 0.7944 (mt-10) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.9195 time to fit residues: 42.8756 Evaluate side-chains 43 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.065134 restraints weight = 8530.362| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.10 r_work: 0.2809 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4093 Z= 0.377 Angle : 0.588 6.707 5571 Z= 0.304 Chirality : 0.043 0.149 621 Planarity : 0.004 0.051 730 Dihedral : 5.366 38.323 630 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.91 % Allowed : 18.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.38), residues: 536 helix: 1.09 (0.45), residues: 149 sheet: -0.60 (0.42), residues: 139 loop : 0.10 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.016 0.002 PHE D 92 TYR 0.010 0.001 TYR D 417 ARG 0.009 0.001 ARG D 201 ********************** 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 46 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9149 (m) cc_final: 0.8577 (p) REVERT: C 38 MET cc_start: 0.8118 (mmt) cc_final: 0.6951 (mmm) REVERT: C 57 SER cc_start: 0.9088 (p) cc_final: 0.8318 (t) REVERT: C 64 TYR cc_start: 0.8276 (m-80) cc_final: 0.7654 (m-80) REVERT: C 84 TYR cc_start: 0.8297 (m-10) cc_final: 0.7960 (m-80) REVERT: C 85 LEU cc_start: 0.7788 (tt) cc_final: 0.7354 (tt) REVERT: D 98 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8808 (p90) REVERT: D 242 GLU cc_start: 0.8829 (pm20) cc_final: 0.8297 (pm20) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.9898 time to fit residues: 45.8594 Evaluate side-chains 43 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 40.0000 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.093543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066512 restraints weight = 8290.309| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.09 r_work: 0.2847 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4093 Z= 0.165 Angle : 0.506 6.320 5571 Z= 0.263 Chirality : 0.041 0.139 621 Planarity : 0.004 0.049 730 Dihedral : 4.955 36.603 630 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.19 % Allowed : 18.03 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.39), residues: 536 helix: 1.26 (0.45), residues: 151 sheet: -0.56 (0.44), residues: 132 loop : 0.11 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 233 HIS 0.002 0.001 HIS D 250 PHE 0.016 0.001 PHE D 92 TYR 0.007 0.001 TYR D 360 ARG 0.009 0.001 ARG D 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.69 seconds wall clock time: 51 minutes 12.45 seconds (3072.45 seconds total)