Starting phenix.real_space_refine on Wed Sep 17 04:23:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rnn_24580/09_2025/7rnn_24580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rnn_24580/09_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_24580/09_2025/7rnn_24580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rnn_24580/09_2025/7rnn_24580.map" model { file = "/net/cci-nas-00/data/ceres_data/7rnn_24580/09_2025/7rnn_24580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rnn_24580/09_2025/7rnn_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-2.0-5805/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.29, per 1000 atoms: 0.32 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: 0.39 Conformation dependent library (CDL) restraints added in 172.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.19 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: 0.67 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.580 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:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.660 ------------------------------------------------------------------------------- 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 : 0.013 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 : 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 covalent geometry : bond 0.00797 ( 4093) covalent geometry : angle 0.80440 ( 5571) SS BOND : bond 0.00965 ( 7) SS BOND : angle 3.00584 ( 14) hydrogen bonds : bond 0.17814 ( 187) hydrogen bonds : angle 7.80325 ( 531) link_NAG-ASN : bond 0.48800 ( 2) link_NAG-ASN : angle 42.72786 ( 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: 0.5300 time to fit residues: 36.2602 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 : 0.118 ------------------------------------------------------------------------------- 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... 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 = 0.3540 r_free = 0.3540 target = 0.095378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.068123 restraints weight = 8595.468| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.13 r_work: 0.2874 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4102 Z= 0.120 Angle : 0.685 12.495 5591 Z= 0.331 Chirality : 0.041 0.144 621 Planarity : 0.004 0.044 730 Dihedral : 7.960 57.045 631 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.37 % Allowed : 9.02 % Favored : 89.62 % 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 aren not related in a simple way. whole: -0.32 (0.38), residues: 536 helix: 0.47 (0.44), residues: 144 sheet: -0.58 (0.44), residues: 139 loop : -0.24 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 204 TYR 0.020 0.001 TYR D 360 PHE 0.012 0.001 PHE D 352 TRP 0.007 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 4093) covalent geometry : angle 0.63390 ( 5571) SS BOND : bond 0.00183 ( 7) SS BOND : angle 2.04937 ( 14) hydrogen bonds : bond 0.03748 ( 187) hydrogen bonds : angle 5.57961 ( 531) link_NAG-ASN : bond 0.00934 ( 2) link_NAG-ASN : angle 7.40564 ( 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 : 0.126 Fit side-chains revert: symmetry clash REVERT: C 38 MET cc_start: 0.8820 (mmm) cc_final: 0.8464 (mmm) REVERT: C 64 TYR cc_start: 0.8567 (m-80) cc_final: 0.7991 (m-80) REVERT: C 77 ASP cc_start: 0.8081 (t0) cc_final: 0.7751 (t0) REVERT: C 84 TYR cc_start: 0.8340 (m-10) cc_final: 0.8018 (m-80) REVERT: C 85 LEU cc_start: 0.8049 (tt) cc_final: 0.7614 (tt) REVERT: D 129 MET cc_start: -0.0031 (mmm) cc_final: -0.0756 (ptm) REVERT: D 365 MET cc_start: 0.8699 (ttp) cc_final: 0.8335 (ttm) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.5067 time to fit residues: 28.4197 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 : 0.098 ------------------------------------------------------------------------------- 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: 5.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.094557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067722 restraints weight = 8362.736| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.13 r_work: 0.2865 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4102 Z= 0.139 Angle : 0.585 8.528 5591 Z= 0.292 Chirality : 0.041 0.150 621 Planarity : 0.004 0.042 730 Dihedral : 5.811 54.965 631 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.19 % Allowed : 13.11 % Favored : 84.70 % 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 aren not related in a simple way. whole: 0.13 (0.39), residues: 536 helix: 0.96 (0.45), residues: 144 sheet: -0.36 (0.44), residues: 145 loop : -0.00 (0.44), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 201 TYR 0.015 0.001 TYR D 360 PHE 0.007 0.001 PHE D 241 TRP 0.005 0.001 TRP D 233 HIS 0.005 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4093) covalent geometry : angle 0.55416 ( 5571) SS BOND : bond 0.00168 ( 7) SS BOND : angle 1.96983 ( 14) hydrogen bonds : bond 0.03207 ( 187) hydrogen bonds : angle 4.95124 ( 531) link_NAG-ASN : bond 0.00350 ( 2) link_NAG-ASN : angle 4.97825 ( 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 55 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: C 33 PHE cc_start: 0.6230 (p90) cc_final: 0.5974 (p90) REVERT: C 38 MET cc_start: 0.8934 (mmm) cc_final: 0.8549 (mmm) REVERT: C 64 TYR cc_start: 0.8540 (m-80) cc_final: 0.7811 (m-80) REVERT: C 81 ASN cc_start: 0.8677 (m-40) cc_final: 0.8338 (m-40) REVERT: C 85 LEU cc_start: 0.7847 (tt) cc_final: 0.7502 (tt) REVERT: D 98 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8670 (p90) REVERT: D 129 MET cc_start: 0.0790 (mmm) cc_final: -0.0355 (ptm) REVERT: D 242 GLU cc_start: 0.8759 (pm20) cc_final: 0.8318 (pm20) REVERT: D 365 MET cc_start: 0.8551 (ttp) cc_final: 0.8156 (ttm) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.5000 time to fit residues: 26.0336 Evaluate side-chains 46 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.093096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.065954 restraints weight = 8446.614| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.13 r_work: 0.2832 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4102 Z= 0.181 Angle : 0.583 8.622 5591 Z= 0.295 Chirality : 0.041 0.142 621 Planarity : 0.004 0.039 730 Dihedral : 5.537 47.744 631 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.46 % Allowed : 15.30 % Favored : 82.24 % 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 aren not related in a simple way. whole: 0.20 (0.39), residues: 536 helix: 1.19 (0.46), residues: 142 sheet: -0.43 (0.43), residues: 145 loop : 0.02 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 201 TYR 0.012 0.001 TYR C 104 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 covalent geometry : bond 0.00413 ( 4093) covalent geometry : angle 0.55555 ( 5571) SS BOND : bond 0.00181 ( 7) SS BOND : angle 1.78426 ( 14) hydrogen bonds : bond 0.03207 ( 187) hydrogen bonds : angle 4.90511 ( 531) link_NAG-ASN : bond 0.00313 ( 2) link_NAG-ASN : angle 4.72239 ( 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 48 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.117 Fit side-chains REVERT: C 34 SER cc_start: 0.9073 (m) cc_final: 0.8741 (p) REVERT: C 64 TYR cc_start: 0.8397 (m-80) cc_final: 0.7835 (m-80) REVERT: C 84 TYR cc_start: 0.8242 (m-10) cc_final: 0.7909 (m-80) REVERT: C 85 LEU cc_start: 0.7904 (tt) cc_final: 0.7538 (tt) REVERT: D 98 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8757 (p90) REVERT: D 154 MET cc_start: 0.8969 (mmt) cc_final: 0.8749 (tpp) REVERT: D 242 GLU cc_start: 0.8823 (pm20) cc_final: 0.8315 (pm20) REVERT: D 365 MET cc_start: 0.8454 (ttp) cc_final: 0.8036 (ttm) outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.4583 time to fit residues: 21.5461 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 75 THR Chi-restraints excluded: chain D residue 98 PHE 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: 9.9990 chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.0030 chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.092586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.065523 restraints weight = 8539.922| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.13 r_work: 0.2822 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4102 Z= 0.204 Angle : 0.595 8.281 5591 Z= 0.301 Chirality : 0.042 0.143 621 Planarity : 0.004 0.042 730 Dihedral : 5.213 37.425 630 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.01 % Allowed : 15.30 % Favored : 81.69 % 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 aren not related in a simple way. whole: 0.17 (0.38), residues: 536 helix: 1.23 (0.45), residues: 144 sheet: -0.50 (0.43), residues: 146 loop : -0.01 (0.44), residues: 246 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 257 TRP 0.006 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 4093) covalent geometry : angle 0.56630 ( 5571) SS BOND : bond 0.00234 ( 7) SS BOND : angle 2.26163 ( 14) hydrogen bonds : bond 0.03257 ( 187) hydrogen bonds : angle 4.85154 ( 531) link_NAG-ASN : bond 0.00253 ( 2) link_NAG-ASN : angle 4.53748 ( 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 52 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.166 Fit side-chains REVERT: C 34 SER cc_start: 0.9100 (m) cc_final: 0.8535 (p) REVERT: C 57 SER cc_start: 0.9148 (p) cc_final: 0.8500 (t) REVERT: C 64 TYR cc_start: 0.8283 (m-80) cc_final: 0.7679 (m-80) REVERT: C 84 TYR cc_start: 0.8250 (m-10) cc_final: 0.7886 (m-80) REVERT: C 85 LEU cc_start: 0.7871 (tt) cc_final: 0.7517 (tt) REVERT: D 98 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8752 (p90) REVERT: D 242 GLU cc_start: 0.8824 (pm20) cc_final: 0.8331 (pm20) REVERT: D 365 MET cc_start: 0.8416 (ttp) cc_final: 0.7980 (ttm) outliers start: 11 outliers final: 5 residues processed: 50 average time/residue: 0.4090 time to fit residues: 21.4866 Evaluate side-chains 46 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 447 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.092960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065958 restraints weight = 8440.300| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.11 r_work: 0.2829 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4102 Z= 0.162 Angle : 0.557 7.960 5591 Z= 0.282 Chirality : 0.041 0.140 621 Planarity : 0.003 0.039 730 Dihedral : 5.082 37.244 630 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.19 % Allowed : 16.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.39), residues: 536 helix: 1.43 (0.46), residues: 142 sheet: -0.48 (0.43), residues: 146 loop : 0.06 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 201 TYR 0.007 0.001 TYR D 417 PHE 0.006 0.001 PHE D 263 TRP 0.007 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4093) covalent geometry : angle 0.53055 ( 5571) SS BOND : bond 0.00134 ( 7) SS BOND : angle 1.97655 ( 14) hydrogen bonds : bond 0.03103 ( 187) hydrogen bonds : angle 4.73563 ( 531) link_NAG-ASN : bond 0.00178 ( 2) link_NAG-ASN : angle 4.36941 ( 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: 8 poor density : 42 time to evaluate : 0.151 Fit side-chains REVERT: C 34 SER cc_start: 0.9087 (m) cc_final: 0.8541 (p) REVERT: C 57 SER cc_start: 0.9086 (p) cc_final: 0.8356 (t) REVERT: C 64 TYR cc_start: 0.8257 (m-80) cc_final: 0.7591 (m-80) REVERT: C 84 TYR cc_start: 0.8239 (m-10) cc_final: 0.7928 (m-80) REVERT: C 85 LEU cc_start: 0.7911 (tt) cc_final: 0.7436 (tt) REVERT: D 98 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8758 (p90) REVERT: D 242 GLU cc_start: 0.8803 (pm20) cc_final: 0.8322 (pm20) REVERT: D 345 CYS cc_start: 0.5470 (OUTLIER) cc_final: 0.5025 (t) REVERT: D 365 MET cc_start: 0.8427 (ttp) cc_final: 0.7976 (ttm) REVERT: D 418 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7966 (mt-10) outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 0.4809 time to fit residues: 24.1012 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 : 0.164 ------------------------------------------------------------------------------- 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: 6.9990 chunk 6 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.093419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.066297 restraints weight = 8574.852| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.15 r_work: 0.2843 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4102 Z= 0.127 Angle : 0.536 7.474 5591 Z= 0.272 Chirality : 0.040 0.137 621 Planarity : 0.003 0.046 730 Dihedral : 4.923 37.146 630 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 17.76 % 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 aren not related in a simple way. whole: 0.33 (0.39), residues: 536 helix: 1.24 (0.45), residues: 150 sheet: -0.39 (0.44), residues: 139 loop : 0.11 (0.44), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 201 TYR 0.007 0.001 TYR D 417 PHE 0.009 0.001 PHE C 72 TRP 0.008 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4093) covalent geometry : angle 0.51177 ( 5571) SS BOND : bond 0.00143 ( 7) SS BOND : angle 1.76400 ( 14) hydrogen bonds : bond 0.03015 ( 187) hydrogen bonds : angle 4.68693 ( 531) link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 4.20866 ( 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 : 0.169 Fit side-chains REVERT: C 34 SER cc_start: 0.9115 (m) cc_final: 0.8545 (p) REVERT: C 57 SER cc_start: 0.9118 (p) cc_final: 0.8344 (t) REVERT: C 64 TYR cc_start: 0.8326 (m-80) cc_final: 0.7604 (m-80) REVERT: C 72 PHE cc_start: 0.8300 (m-80) cc_final: 0.8083 (m-80) REVERT: C 85 LEU cc_start: 0.7966 (tt) cc_final: 0.7498 (tt) REVERT: D 98 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8791 (p90) REVERT: D 242 GLU cc_start: 0.8744 (pm20) cc_final: 0.8259 (pm20) REVERT: D 345 CYS cc_start: 0.5360 (OUTLIER) cc_final: 0.4931 (t) REVERT: D 365 MET cc_start: 0.8411 (ttp) cc_final: 0.7998 (ttm) REVERT: D 418 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7968 (mt-10) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.4982 time to fit residues: 23.9206 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 : 0.180 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 35 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.091828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.064642 restraints weight = 8415.547| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.13 r_work: 0.2804 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4102 Z= 0.258 Angle : 0.623 8.434 5591 Z= 0.316 Chirality : 0.043 0.144 621 Planarity : 0.004 0.049 730 Dihedral : 5.393 38.337 630 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.73 % Allowed : 17.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.38), residues: 536 helix: 1.41 (0.46), residues: 142 sheet: -0.48 (0.42), residues: 146 loop : 0.13 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 201 TYR 0.011 0.002 TYR C 99 PHE 0.015 0.002 PHE C 72 TRP 0.008 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 4093) covalent geometry : angle 0.59680 ( 5571) SS BOND : bond 0.00244 ( 7) SS BOND : angle 2.19596 ( 14) hydrogen bonds : bond 0.03472 ( 187) hydrogen bonds : angle 4.87304 ( 531) link_NAG-ASN : bond 0.00303 ( 2) link_NAG-ASN : angle 4.46531 ( 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: 10 poor density : 38 time to evaluate : 0.161 Fit side-chains REVERT: C 33 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.6463 (p90) REVERT: C 34 SER cc_start: 0.9121 (m) cc_final: 0.8603 (p) REVERT: C 57 SER cc_start: 0.9076 (p) cc_final: 0.8301 (t) REVERT: C 84 TYR cc_start: 0.8197 (m-10) cc_final: 0.7858 (m-80) REVERT: C 85 LEU cc_start: 0.7801 (tt) cc_final: 0.7337 (tt) REVERT: D 98 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8802 (p90) REVERT: D 242 GLU cc_start: 0.8829 (pm20) cc_final: 0.8305 (pm20) REVERT: D 345 CYS cc_start: 0.5607 (OUTLIER) cc_final: 0.5076 (t) REVERT: D 365 MET cc_start: 0.8428 (ttp) cc_final: 0.7975 (ttm) outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 0.3669 time to fit residues: 17.1315 Evaluate side-chains 45 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 33 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.093574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.066510 restraints weight = 8540.594| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.13 r_work: 0.2842 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3013 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= 0.119 Angle : 0.534 7.449 5591 Z= 0.272 Chirality : 0.040 0.137 621 Planarity : 0.003 0.041 730 Dihedral : 4.952 36.767 630 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.39), residues: 536 helix: 1.31 (0.45), residues: 150 sheet: -0.43 (0.45), residues: 132 loop : 0.09 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 201 TYR 0.010 0.001 TYR C 99 PHE 0.006 0.001 PHE D 50 TRP 0.009 0.001 TRP D 233 HIS 0.002 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4093) covalent geometry : angle 0.50953 ( 5571) SS BOND : bond 0.00171 ( 7) SS BOND : angle 1.76188 ( 14) hydrogen bonds : bond 0.03049 ( 187) hydrogen bonds : angle 4.66036 ( 531) link_NAG-ASN : bond 0.00126 ( 2) link_NAG-ASN : angle 4.19406 ( 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 49 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.115 Fit side-chains REVERT: C 34 SER cc_start: 0.9130 (m) cc_final: 0.8568 (p) REVERT: C 57 SER cc_start: 0.9083 (p) cc_final: 0.8253 (t) REVERT: C 84 TYR cc_start: 0.8211 (m-10) cc_final: 0.7889 (m-80) REVERT: C 85 LEU cc_start: 0.7824 (tt) cc_final: 0.7388 (tt) REVERT: D 242 GLU cc_start: 0.8779 (pm20) cc_final: 0.8279 (pm20) REVERT: D 345 CYS cc_start: 0.5492 (OUTLIER) cc_final: 0.4999 (t) REVERT: D 365 MET cc_start: 0.8381 (ttp) cc_final: 0.7951 (ttm) REVERT: D 418 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7952 (mt-10) outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 0.4150 time to fit residues: 20.1223 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 : 0.173 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.094424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.067337 restraints weight = 8279.762| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.08 r_work: 0.2855 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4102 Z= 0.121 Angle : 0.535 7.279 5591 Z= 0.272 Chirality : 0.040 0.138 621 Planarity : 0.003 0.042 730 Dihedral : 4.860 36.990 630 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.37 % Allowed : 19.67 % Favored : 78.96 % 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 aren not related in a simple way. whole: 0.42 (0.39), residues: 536 helix: 1.39 (0.46), residues: 149 sheet: -0.40 (0.45), residues: 132 loop : 0.12 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 201 TYR 0.007 0.001 TYR D 360 PHE 0.008 0.001 PHE C 33 TRP 0.008 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4093) covalent geometry : angle 0.51194 ( 5571) SS BOND : bond 0.00180 ( 7) SS BOND : angle 1.68918 ( 14) hydrogen bonds : bond 0.03016 ( 187) hydrogen bonds : angle 4.60564 ( 531) link_NAG-ASN : bond 0.00086 ( 2) link_NAG-ASN : angle 4.12601 ( 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: 5 poor density : 39 time to evaluate : 0.162 Fit side-chains REVERT: C 34 SER cc_start: 0.9199 (m) cc_final: 0.8595 (p) REVERT: C 38 MET cc_start: 0.7876 (mmt) cc_final: 0.6768 (mmm) REVERT: C 57 SER cc_start: 0.9093 (p) cc_final: 0.8305 (t) REVERT: C 84 TYR cc_start: 0.8265 (m-10) cc_final: 0.7927 (m-80) REVERT: C 85 LEU cc_start: 0.7825 (tt) cc_final: 0.7398 (tt) REVERT: D 242 GLU cc_start: 0.8766 (pm20) cc_final: 0.8279 (pm20) REVERT: D 345 CYS cc_start: 0.5602 (OUTLIER) cc_final: 0.5116 (t) REVERT: D 418 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7955 (mt-10) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.3920 time to fit residues: 17.4003 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 : 0.175 ------------------------------------------------------------------------------- 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 86 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 8 optimal weight: 0.0570 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 50 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 overall best weight: 0.3096 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.095806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068863 restraints weight = 8400.247| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.15 r_work: 0.2909 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3296 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= 0.086 Angle : 0.493 6.431 5591 Z= 0.252 Chirality : 0.040 0.134 621 Planarity : 0.003 0.037 730 Dihedral : 4.357 35.652 630 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.91 % Allowed : 18.85 % 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 aren not related in a simple way. whole: 0.53 (0.39), residues: 536 helix: 1.57 (0.46), residues: 151 sheet: -0.30 (0.47), residues: 132 loop : 0.10 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 201 TYR 0.005 0.001 TYR D 417 PHE 0.006 0.001 PHE D 50 TRP 0.008 0.001 TRP C 40 HIS 0.002 0.000 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00184 ( 4093) covalent geometry : angle 0.47307 ( 5571) SS BOND : bond 0.00144 ( 7) SS BOND : angle 1.41594 ( 14) hydrogen bonds : bond 0.02889 ( 187) hydrogen bonds : angle 4.55145 ( 531) link_NAG-ASN : bond 0.00104 ( 2) link_NAG-ASN : angle 3.78022 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1528.06 seconds wall clock time: 26 minutes 50.40 seconds (1610.40 seconds total)