Starting phenix.real_space_refine on Wed Jul 23 18:54:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rnn_24580/07_2025/7rnn_24580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rnn_24580/07_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_24580/07_2025/7rnn_24580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rnn_24580/07_2025/7rnn_24580.map" model { file = "/net/cci-nas-00/data/ceres_data/7rnn_24580/07_2025/7rnn_24580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rnn_24580/07_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-5711/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: 3.50, per 1000 atoms: 0.88 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: 1.02 Conformation dependent library (CDL) restraints added in 514.9 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: 0.55 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: 1.15 Time building geometry restraints manager: 1.23 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: 2.140 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.48800 ( 2) link_NAG-ASN : angle 42.72786 ( 6) hydrogen bonds : bond 0.17814 ( 187) hydrogen bonds : angle 7.80325 ( 531) SS BOND : bond 0.00965 ( 7) SS BOND : angle 3.00584 ( 14) covalent geometry : bond 0.00797 ( 4093) covalent geometry : angle 0.80440 ( 5571) *********************** 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 : 0.486 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: 1.0364 time to fit residues: 71.1752 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 : 0.443 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.068139 restraints weight = 8437.518| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.12 r_work: 0.2881 rms_B_bonded: 3.23 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 4102 Z= 0.124 Angle : 0.678 11.406 5591 Z= 0.328 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00947 ( 2) link_NAG-ASN : angle 6.95698 ( 6) hydrogen bonds : bond 0.03595 ( 187) hydrogen bonds : angle 5.47073 ( 531) SS BOND : bond 0.00211 ( 7) SS BOND : angle 2.11062 ( 14) covalent geometry : bond 0.00256 ( 4093) covalent geometry : angle 0.63093 ( 5571) *********************** 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 : 0.429 Fit side-chains REVERT: C 38 MET cc_start: 0.8850 (mmm) cc_final: 0.8470 (mmm) REVERT: C 64 TYR cc_start: 0.8573 (m-80) cc_final: 0.7994 (m-80) REVERT: C 72 PHE cc_start: 0.8465 (m-80) cc_final: 0.8224 (m-80) REVERT: C 77 ASP cc_start: 0.8064 (t0) cc_final: 0.7725 (t0) REVERT: C 84 TYR cc_start: 0.8323 (m-10) cc_final: 0.8065 (m-80) REVERT: C 85 LEU cc_start: 0.8040 (tt) cc_final: 0.7621 (tt) REVERT: D 129 MET cc_start: 0.0306 (mmm) cc_final: -0.0600 (ptm) REVERT: D 365 MET cc_start: 0.8635 (ttp) cc_final: 0.8292 (ttm) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.9745 time to fit residues: 54.1345 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 : 0.493 ------------------------------------------------------------------------------- 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: 3.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.094118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066803 restraints weight = 8422.662| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.17 r_work: 0.2848 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4102 Z= 0.160 Angle : 0.588 8.590 5591 Z= 0.295 Chirality : 0.041 0.147 621 Planarity : 0.004 0.040 730 Dihedral : 5.437 34.897 630 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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 (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: 0.14 (0.39), residues: 536 helix: 0.94 (0.45), residues: 143 sheet: -0.40 (0.44), residues: 145 loop : 0.07 (0.44), residues: 248 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 0.007 0.001 PHE D 241 TYR 0.015 0.001 TYR D 360 ARG 0.007 0.001 ARG D 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 2) link_NAG-ASN : angle 5.06773 ( 6) hydrogen bonds : bond 0.03259 ( 187) hydrogen bonds : angle 4.98519 ( 531) SS BOND : bond 0.00150 ( 7) SS BOND : angle 1.52421 ( 14) covalent geometry : bond 0.00363 ( 4093) covalent geometry : angle 0.55944 ( 5571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9088 (m) cc_final: 0.8706 (p) REVERT: C 38 MET cc_start: 0.8906 (mmm) cc_final: 0.8584 (mmm) REVERT: C 64 TYR cc_start: 0.8539 (m-80) cc_final: 0.7796 (m-80) REVERT: C 81 ASN cc_start: 0.8614 (m-40) cc_final: 0.8385 (m-40) REVERT: C 85 LEU cc_start: 0.7839 (tt) cc_final: 0.7498 (tt) REVERT: D 98 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8609 (p90) REVERT: D 129 MET cc_start: 0.1016 (mmm) cc_final: -0.0223 (ptm) REVERT: D 242 GLU cc_start: 0.8778 (pm20) cc_final: 0.8335 (pm20) REVERT: D 365 MET cc_start: 0.8559 (ttp) cc_final: 0.8155 (ttm) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 1.0028 time to fit residues: 50.2998 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 : 0.434 ------------------------------------------------------------------------------- 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: 5.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.094216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.067146 restraints weight = 8369.109| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.13 r_work: 0.2862 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4102 Z= 0.107 Angle : 0.531 7.875 5591 Z= 0.267 Chirality : 0.040 0.142 621 Planarity : 0.004 0.039 730 Dihedral : 4.878 32.593 630 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.64 % Allowed : 15.85 % Favored : 82.51 % 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: 0.13 (0.39), residues: 536 helix: 0.82 (0.45), residues: 151 sheet: -0.33 (0.45), residues: 140 loop : 0.05 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 40 HIS 0.003 0.001 HIS D 250 PHE 0.006 0.001 PHE D 50 TYR 0.009 0.001 TYR D 360 ARG 0.008 0.001 ARG D 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 2) link_NAG-ASN : angle 4.62325 ( 6) hydrogen bonds : bond 0.02940 ( 187) hydrogen bonds : angle 4.78634 ( 531) SS BOND : bond 0.00171 ( 7) SS BOND : angle 1.27220 ( 14) covalent geometry : bond 0.00237 ( 4093) covalent geometry : angle 0.50535 ( 5571) *********************** 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 45 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: C 64 TYR cc_start: 0.8543 (m-80) cc_final: 0.7865 (m-80) REVERT: C 81 ASN cc_start: 0.8662 (m-40) cc_final: 0.8386 (m-40) REVERT: C 84 TYR cc_start: 0.8265 (m-10) cc_final: 0.7906 (m-80) REVERT: C 85 LEU cc_start: 0.7897 (tt) cc_final: 0.7544 (tt) REVERT: D 98 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8679 (p90) REVERT: D 242 GLU cc_start: 0.8756 (pm20) cc_final: 0.8303 (pm20) REVERT: D 365 MET cc_start: 0.8501 (ttp) cc_final: 0.8067 (ttm) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 1.0284 time to fit residues: 46.3467 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 : 0.483 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 36 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.093174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.066127 restraints weight = 8562.007| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.14 r_work: 0.2837 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4102 Z= 0.153 Angle : 0.544 7.972 5591 Z= 0.274 Chirality : 0.041 0.142 621 Planarity : 0.004 0.038 730 Dihedral : 4.867 35.091 630 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.19 % Allowed : 16.12 % 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 (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: 0.21 (0.39), residues: 536 helix: 0.95 (0.45), residues: 151 sheet: -0.35 (0.45), residues: 139 loop : 0.09 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 40 HIS 0.003 0.001 HIS D 250 PHE 0.006 0.001 PHE D 257 TYR 0.012 0.001 TYR C 99 ARG 0.010 0.001 ARG D 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 2) link_NAG-ASN : angle 4.45916 ( 6) hydrogen bonds : bond 0.03060 ( 187) hydrogen bonds : angle 4.73764 ( 531) SS BOND : bond 0.00155 ( 7) SS BOND : angle 1.42204 ( 14) covalent geometry : bond 0.00352 ( 4093) covalent geometry : angle 0.51996 ( 5571) *********************** 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: 8 poor density : 39 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9078 (m) cc_final: 0.8706 (p) REVERT: C 38 MET cc_start: 0.8177 (mmt) cc_final: 0.7542 (mmm) REVERT: C 64 TYR cc_start: 0.8398 (m-80) cc_final: 0.7767 (m-80) REVERT: C 84 TYR cc_start: 0.8249 (m-10) cc_final: 0.7911 (m-80) REVERT: C 85 LEU cc_start: 0.7861 (tt) cc_final: 0.7484 (tt) REVERT: D 84 GLN cc_start: 0.8696 (mt0) cc_final: 0.8464 (mt0) REVERT: D 98 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8714 (p90) REVERT: D 242 GLU cc_start: 0.8793 (pm20) cc_final: 0.8293 (pm20) REVERT: D 365 MET cc_start: 0.8460 (ttp) cc_final: 0.8006 (ttm) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 1.2631 time to fit residues: 59.5136 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 : 0.467 ------------------------------------------------------------------------------- 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: 4.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.092913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.065915 restraints weight = 8580.699| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.13 r_work: 0.2826 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4102 Z= 0.183 Angle : 0.561 7.955 5591 Z= 0.284 Chirality : 0.041 0.144 621 Planarity : 0.004 0.045 730 Dihedral : 5.073 36.232 630 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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 (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: 0.37 (0.39), residues: 536 helix: 1.39 (0.46), residues: 143 sheet: -0.37 (0.43), residues: 146 loop : 0.10 (0.43), residues: 247 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 0.007 0.001 PHE D 241 TYR 0.010 0.001 TYR D 360 ARG 0.009 0.001 ARG D 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 2) link_NAG-ASN : angle 4.39793 ( 6) hydrogen bonds : bond 0.03140 ( 187) hydrogen bonds : angle 4.76691 ( 531) SS BOND : bond 0.00195 ( 7) SS BOND : angle 1.56269 ( 14) covalent geometry : bond 0.00422 ( 4093) covalent geometry : angle 0.53745 ( 5571) *********************** 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 52 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9096 (m) cc_final: 0.8515 (p) REVERT: C 57 SER cc_start: 0.9136 (p) cc_final: 0.8461 (t) REVERT: C 64 TYR cc_start: 0.8271 (m-80) cc_final: 0.7576 (m-80) REVERT: C 84 TYR cc_start: 0.8236 (m-10) cc_final: 0.7904 (m-80) REVERT: C 85 LEU cc_start: 0.7858 (tt) cc_final: 0.7482 (tt) REVERT: D 98 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8768 (p90) REVERT: D 242 GLU cc_start: 0.8795 (pm20) cc_final: 0.8306 (pm20) REVERT: D 365 MET cc_start: 0.8434 (ttp) cc_final: 0.7985 (ttm) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.8775 time to fit residues: 46.2527 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 : 0.461 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.091982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.064795 restraints weight = 8468.028| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.13 r_work: 0.2807 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4102 Z= 0.229 Angle : 0.594 8.402 5591 Z= 0.301 Chirality : 0.042 0.144 621 Planarity : 0.004 0.043 730 Dihedral : 5.278 37.139 630 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.73 % Allowed : 16.67 % 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: 0.22 (0.38), residues: 536 helix: 1.09 (0.46), residues: 149 sheet: -0.42 (0.43), residues: 140 loop : 0.05 (0.43), residues: 247 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 0.011 0.001 PHE C 72 TYR 0.012 0.001 TYR C 99 ARG 0.009 0.001 ARG D 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 2) link_NAG-ASN : angle 4.47101 ( 6) hydrogen bonds : bond 0.03314 ( 187) hydrogen bonds : angle 4.82059 ( 531) SS BOND : bond 0.00241 ( 7) SS BOND : angle 1.71273 ( 14) covalent geometry : bond 0.00529 ( 4093) covalent geometry : angle 0.57019 ( 5571) *********************** 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: 10 poor density : 40 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9131 (m) cc_final: 0.8538 (p) REVERT: C 57 SER cc_start: 0.9078 (p) cc_final: 0.8373 (t) REVERT: C 64 TYR cc_start: 0.8302 (m-80) cc_final: 0.7703 (m-80) REVERT: C 85 LEU cc_start: 0.7892 (tt) cc_final: 0.7489 (tt) REVERT: D 98 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8742 (p90) REVERT: D 242 GLU cc_start: 0.8842 (pm20) cc_final: 0.8359 (pm20) REVERT: D 365 MET cc_start: 0.8421 (ttp) cc_final: 0.7976 (ttm) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 1.2607 time to fit residues: 63.7099 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 : 0.500 ------------------------------------------------------------------------------- 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: 8.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.093221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.066120 restraints weight = 8241.102| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.09 r_work: 0.2841 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2858 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= 0.131 Angle : 0.539 7.517 5591 Z= 0.274 Chirality : 0.040 0.138 621 Planarity : 0.004 0.045 730 Dihedral : 4.961 36.464 630 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 18.31 % 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 (0.39), residues: 536 helix: 1.23 (0.46), residues: 149 sheet: -0.34 (0.46), residues: 132 loop : 0.07 (0.43), residues: 255 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 0.010 0.001 PHE C 72 TYR 0.007 0.001 TYR D 389 ARG 0.010 0.001 ARG C 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 2) link_NAG-ASN : angle 4.23576 ( 6) hydrogen bonds : bond 0.02995 ( 187) hydrogen bonds : angle 4.67552 ( 531) SS BOND : bond 0.00195 ( 7) SS BOND : angle 1.38004 ( 14) covalent geometry : bond 0.00300 ( 4093) covalent geometry : angle 0.51666 ( 5571) *********************** 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: 7 poor density : 41 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9126 (m) cc_final: 0.8520 (p) REVERT: C 57 SER cc_start: 0.9112 (p) cc_final: 0.8310 (t) REVERT: C 64 TYR cc_start: 0.8274 (m-80) cc_final: 0.7806 (m-80) REVERT: C 84 TYR cc_start: 0.8225 (m-10) cc_final: 0.7871 (m-80) REVERT: C 85 LEU cc_start: 0.7818 (tt) cc_final: 0.7460 (tt) REVERT: D 98 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8751 (p90) REVERT: D 242 GLU cc_start: 0.8738 (pm20) cc_final: 0.8227 (pm20) REVERT: D 365 MET cc_start: 0.8385 (ttp) cc_final: 0.7955 (ttm) REVERT: D 418 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7941 (mt-10) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.9115 time to fit residues: 44.1496 Evaluate side-chains 45 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 0.0670 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 3 optimal weight: 9.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.094766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.067964 restraints weight = 8418.870| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.08 r_work: 0.2870 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4102 Z= 0.098 Angle : 0.515 6.895 5591 Z= 0.260 Chirality : 0.040 0.137 621 Planarity : 0.004 0.047 730 Dihedral : 4.633 36.097 630 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.37 % Allowed : 18.85 % 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: 0.45 (0.39), residues: 536 helix: 1.37 (0.46), residues: 149 sheet: -0.28 (0.46), residues: 132 loop : 0.11 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 233 HIS 0.002 0.001 HIS D 250 PHE 0.008 0.001 PHE C 72 TYR 0.006 0.001 TYR D 417 ARG 0.017 0.001 ARG C 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 4.03385 ( 6) hydrogen bonds : bond 0.02776 ( 187) hydrogen bonds : angle 4.52588 ( 531) SS BOND : bond 0.00160 ( 7) SS BOND : angle 1.17545 ( 14) covalent geometry : bond 0.00218 ( 4093) covalent geometry : angle 0.49481 ( 5571) *********************** 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 48 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9163 (m) cc_final: 0.8538 (p) REVERT: C 57 SER cc_start: 0.9133 (p) cc_final: 0.8341 (t) REVERT: C 64 TYR cc_start: 0.8422 (m-80) cc_final: 0.7724 (m-80) REVERT: C 84 TYR cc_start: 0.8248 (m-10) cc_final: 0.7885 (m-80) REVERT: C 85 LEU cc_start: 0.7803 (tt) cc_final: 0.7412 (tt) REVERT: D 98 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8788 (p90) REVERT: D 242 GLU cc_start: 0.8680 (pm20) cc_final: 0.8182 (pm20) REVERT: D 418 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8055 (mt-10) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 1.1236 time to fit residues: 55.4366 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 : 0.485 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.066464 restraints weight = 8470.766| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.08 r_work: 0.2830 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4102 Z= 0.173 Angle : 0.556 7.504 5591 Z= 0.281 Chirality : 0.041 0.141 621 Planarity : 0.004 0.048 730 Dihedral : 4.896 37.044 630 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.64 % Allowed : 19.40 % 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 (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: 0.43 (0.39), residues: 536 helix: 1.32 (0.46), residues: 149 sheet: -0.25 (0.45), residues: 132 loop : 0.11 (0.43), residues: 255 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 0.012 0.001 PHE C 72 TYR 0.011 0.001 TYR C 99 ARG 0.016 0.001 ARG C 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 2) link_NAG-ASN : angle 4.14438 ( 6) hydrogen bonds : bond 0.03122 ( 187) hydrogen bonds : angle 4.65612 ( 531) SS BOND : bond 0.00188 ( 7) SS BOND : angle 1.46557 ( 14) covalent geometry : bond 0.00399 ( 4093) covalent geometry : angle 0.53530 ( 5571) ********************** 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 45 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: C 34 SER cc_start: 0.9168 (m) cc_final: 0.8555 (p) REVERT: C 57 SER cc_start: 0.9089 (p) cc_final: 0.8299 (t) REVERT: C 64 TYR cc_start: 0.8319 (m-80) cc_final: 0.7620 (m-80) REVERT: C 71 ARG cc_start: 0.7503 (mtp-110) cc_final: 0.7303 (mtp85) REVERT: C 84 TYR cc_start: 0.8226 (m-10) cc_final: 0.7846 (m-80) REVERT: C 85 LEU cc_start: 0.7697 (tt) cc_final: 0.7313 (tt) REVERT: C 105 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7680 (ptp-170) REVERT: D 98 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8798 (p90) REVERT: D 242 GLU cc_start: 0.8768 (pm20) cc_final: 0.8248 (pm20) REVERT: D 418 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7937 (mt-10) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 1.2838 time to fit residues: 57.5959 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 : 0.501 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.067333 restraints weight = 8390.865| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.08 r_work: 0.2852 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4102 Z= 0.119 Angle : 0.525 7.097 5591 Z= 0.265 Chirality : 0.040 0.137 621 Planarity : 0.004 0.052 730 Dihedral : 4.711 36.094 630 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.64 % Allowed : 19.67 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.39), residues: 536 helix: 1.42 (0.46), residues: 149 sheet: -0.20 (0.46), residues: 132 loop : 0.10 (0.43), residues: 255 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 0.008 0.001 PHE C 72 TYR 0.011 0.001 TYR C 99 ARG 0.015 0.001 ARG C 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 4.02217 ( 6) hydrogen bonds : bond 0.02969 ( 187) hydrogen bonds : angle 4.58134 ( 531) SS BOND : bond 0.00154 ( 7) SS BOND : angle 1.23562 ( 14) covalent geometry : bond 0.00270 ( 4093) covalent geometry : angle 0.50529 ( 5571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3237.18 seconds wall clock time: 57 minutes 26.23 seconds (3446.23 seconds total)